<?xml version="1.0" encoding="UTF-8"?>

<!--XBRL Document Created with Wdesk from Workiva-->
<!--Copyright 2022 Workiva-->
<!--r:62b320b8-f1f6-4dd2-9448-7d9217c600d6,g:ef202fdc-24ed-442b-ab9a-9c0b68901b91-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:hqy="http://www.healthequity.com/20220131" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2020-01-21" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://www.healthequity.com/20220131">
  <xs:import namespace="http://fasb.org/srt/2021-01-31" schemaLocation="https://xbrl.fasb.org/srt/2021/elts/srt-2021-01-31.xsd"/>
  <xs:import namespace="http://fasb.org/us-gaap/2021-01-31" schemaLocation="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd"/>
  <xs:import namespace="http://www.w3.org/1999/xlink" schemaLocation="http://www.xbrl.org/2003/xlink-2003-12-31.xsd"/>
  <xs:import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd"/>
  <xs:import namespace="http://www.xbrl.org/2003/linkbase" schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd"/>
  <xs:import namespace="http://www.xbrl.org/dtr/type/2020-01-21" schemaLocation="https://www.xbrl.org/dtr/type/2020-01-21/types.xsd"/>
  <xs:import namespace="http://xbrl.org/2005/xbrldt" schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd"/>
  <xs:import namespace="http://xbrl.sec.gov/dei/2021q4" schemaLocation="https://xbrl.sec.gov/dei/2021q4/dei-2021q4.xsd"/>
  <xs:annotation>
    <xs:appinfo>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="hqy-20220131_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="hqy-20220131_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="hqy-20220131_cal.xml" xlink:role="http://www.xbrl.org/2003/role/calculationLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="hqy-20220131_def.xml" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:type="simple"/>
      <link:roleType id="CoverPage" roleURI="http://www.healthequity.com/role/CoverPage">
        <link:definition>0001001 - Document - Cover Page</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="AuditInformation" roleURI="http://www.healthequity.com/role/AuditInformation">
        <link:definition>0002002 - Document - Audit Information</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ConsolidatedBalanceSheets" roleURI="http://www.healthequity.com/role/ConsolidatedBalanceSheets">
        <link:definition>1001003 - Statement - Consolidated Balance Sheets</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ConsolidatedBalanceSheetsParenthetical" roleURI="http://www.healthequity.com/role/ConsolidatedBalanceSheetsParenthetical">
        <link:definition>1002004 - Statement - Consolidated Balance Sheets (Parenthetical)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ConsolidatedStatementsofOperationsandComprehensiveIncomeLoss" roleURI="http://www.healthequity.com/role/ConsolidatedStatementsofOperationsandComprehensiveIncomeLoss">
        <link:definition>1003005 - Statement - Consolidated Statements of Operations and Comprehensive Income (Loss)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ConsolidatedStatementsofStockholdersEquity" roleURI="http://www.healthequity.com/role/ConsolidatedStatementsofStockholdersEquity">
        <link:definition>1004006 - Statement - Consolidated Statements of Stockholders' Equity</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ConsolidatedStatementsofCashFlows" roleURI="http://www.healthequity.com/role/ConsolidatedStatementsofCashFlows">
        <link:definition>1005007 - Statement - Consolidated Statements of Cash Flows</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Summaryofbusinessandsignificantaccountingpolicies" roleURI="http://www.healthequity.com/role/Summaryofbusinessandsignificantaccountingpolicies">
        <link:definition>2101101 - Disclosure - Summary of business and significant accounting policies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SummaryofbusinessandsignificantaccountingpoliciesPolicies" roleURI="http://www.healthequity.com/role/SummaryofbusinessandsignificantaccountingpoliciesPolicies">
        <link:definition>2202201 - Disclosure - Summary of business and significant accounting policies (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SummaryofbusinessandsignificantaccountingpoliciesTables" roleURI="http://www.healthequity.com/role/SummaryofbusinessandsignificantaccountingpoliciesTables">
        <link:definition>2303301 - Disclosure - Summary of business and significant accounting policies (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SummaryofbusinessandsignificantaccountingpoliciesNarrativeDetails" roleURI="http://www.healthequity.com/role/SummaryofbusinessandsignificantaccountingpoliciesNarrativeDetails">
        <link:definition>2404401 - Disclosure - Summary of business and significant accounting policies - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SummaryofbusinessandsignificantaccountingpoliciesPropertyandEquipmentDetails" roleURI="http://www.healthequity.com/role/SummaryofbusinessandsignificantaccountingpoliciesPropertyandEquipmentDetails">
        <link:definition>2405402 - Disclosure - Summary of business and significant accounting policies - Property and Equipment (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SummaryofbusinessandsignificantaccountingpoliciesIntangibleAssetsDetails" roleURI="http://www.healthequity.com/role/SummaryofbusinessandsignificantaccountingpoliciesIntangibleAssetsDetails">
        <link:definition>2406403 - Disclosure - Summary of business and significant accounting policies - Intangible Assets (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Netincomelosspershare" roleURI="http://www.healthequity.com/role/Netincomelosspershare">
        <link:definition>2107102 - Disclosure - Net income (loss) per share</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NetincomelosspershareTables" roleURI="http://www.healthequity.com/role/NetincomelosspershareTables">
        <link:definition>2308302 - Disclosure - Net income (loss) per share (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NetincomelosspershareDetails" roleURI="http://www.healthequity.com/role/NetincomelosspershareDetails">
        <link:definition>2409404 - Disclosure - Net income (loss) per share (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Businesscombinations" roleURI="http://www.healthequity.com/role/Businesscombinations">
        <link:definition>2110103 - Disclosure - Business combinations</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="BusinesscombinationsTables" roleURI="http://www.healthequity.com/role/BusinesscombinationsTables">
        <link:definition>2311303 - Disclosure - Business combinations (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="BusinesscombinationsNarrativeDetails" roleURI="http://www.healthequity.com/role/BusinesscombinationsNarrativeDetails">
        <link:definition>2412405 - Disclosure - Business combinations - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="BusinesscombinationsPreliminaryAllocationofConsiderationDetails" roleURI="http://www.healthequity.com/role/BusinesscombinationsPreliminaryAllocationofConsiderationDetails">
        <link:definition>2413406 - Disclosure - Business combinations - Preliminary Allocation of Consideration (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="BusinesscombinationsProFormaResultsDetails" roleURI="http://www.healthequity.com/role/BusinesscombinationsProFormaResultsDetails">
        <link:definition>2414407 - Disclosure - Business combinations - Pro Forma Results (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="BusinesscombinationsAcquiredIntangibleAssetsDetails" roleURI="http://www.healthequity.com/role/BusinesscombinationsAcquiredIntangibleAssetsDetails">
        <link:definition>2415408 - Disclosure - Business combinations - Acquired Intangible Assets (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Supplementalfinancialstatementinformation" roleURI="http://www.healthequity.com/role/Supplementalfinancialstatementinformation">
        <link:definition>2116104 - Disclosure - Supplemental financial statement information</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SupplementalfinancialstatementinformationTables" roleURI="http://www.healthequity.com/role/SupplementalfinancialstatementinformationTables">
        <link:definition>2317304 - Disclosure - Supplemental financial statement information (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SupplementalfinancialstatementinformationNarrativeDetails" roleURI="http://www.healthequity.com/role/SupplementalfinancialstatementinformationNarrativeDetails">
        <link:definition>2418409 - Disclosure - Supplemental financial statement information - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SupplementalfinancialstatementinformationNarrativeDetails_1" roleURI="http://www.healthequity.com/role/SupplementalfinancialstatementinformationNarrativeDetails_1">
        <link:definition>2418409 - Disclosure - Supplemental financial statement information - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SupplementalfinancialstatementinformationPropertyandequipmentDetails" roleURI="http://www.healthequity.com/role/SupplementalfinancialstatementinformationPropertyandequipmentDetails">
        <link:definition>2419410 - Disclosure - Supplemental financial statement information - Property and equipment (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SupplementalfinancialstatementinformationOtherexpensenetDetails" roleURI="http://www.healthequity.com/role/SupplementalfinancialstatementinformationOtherexpensenetDetails">
        <link:definition>2420411 - Disclosure - Supplemental financial statement information - Other expense, net (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Leases" roleURI="http://www.healthequity.com/role/Leases">
        <link:definition>2121105 - Disclosure - Leases</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesTables" roleURI="http://www.healthequity.com/role/LeasesTables">
        <link:definition>2322305 - Disclosure - Leases (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesNarrativeDetails" roleURI="http://www.healthequity.com/role/LeasesNarrativeDetails">
        <link:definition>2423412 - Disclosure - Leases - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesLeaseCostDetails" roleURI="http://www.healthequity.com/role/LeasesLeaseCostDetails">
        <link:definition>2424413 - Disclosure - Leases - Lease Cost (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesLeaseLiabilitiesDetails" roleURI="http://www.healthequity.com/role/LeasesLeaseLiabilitiesDetails">
        <link:definition>2425414 - Disclosure - Leases - Lease Liabilities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesSupplementalCashFlowInformationDetails" roleURI="http://www.healthequity.com/role/LeasesSupplementalCashFlowInformationDetails">
        <link:definition>2426415 - Disclosure - Leases - Supplemental Cash Flow Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Intangibleassetsandgoodwill" roleURI="http://www.healthequity.com/role/Intangibleassetsandgoodwill">
        <link:definition>2127106 - Disclosure - Intangible assets and goodwill</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IntangibleassetsandgoodwillTables" roleURI="http://www.healthequity.com/role/IntangibleassetsandgoodwillTables">
        <link:definition>2328306 - Disclosure - Intangible assets and goodwill (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IntangibleassetsandgoodwillScheduleoffinitelivedintangibleassetsDetails" roleURI="http://www.healthequity.com/role/IntangibleassetsandgoodwillScheduleoffinitelivedintangibleassetsDetails">
        <link:definition>2429416 - Disclosure - Intangible assets and goodwill - Schedule of finite-lived intangible assets (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IntangibleassetsandgoodwillNarrativeDetails" roleURI="http://www.healthequity.com/role/IntangibleassetsandgoodwillNarrativeDetails">
        <link:definition>2430417 - Disclosure - Intangible assets and goodwill - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IntangibleassetsandgoodwillScheduleforfutureamortizationexpenseDetails" roleURI="http://www.healthequity.com/role/IntangibleassetsandgoodwillScheduleforfutureamortizationexpenseDetails">
        <link:definition>2431418 - Disclosure - Intangible assets and goodwill - Schedule for future amortization expense (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Commitmentsandcontingencies" roleURI="http://www.healthequity.com/role/Commitmentsandcontingencies">
        <link:definition>2132107 - Disclosure - Commitments and contingencies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CommitmentsandcontingenciesTables" roleURI="http://www.healthequity.com/role/CommitmentsandcontingenciesTables">
        <link:definition>2333307 - Disclosure - Commitments and contingencies (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CommitmentsandcontingenciesOutstandingContractualObligationsDetails" roleURI="http://www.healthequity.com/role/CommitmentsandcontingenciesOutstandingContractualObligationsDetails">
        <link:definition>2434419 - Disclosure - Commitments and contingencies - Outstanding Contractual Obligations (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CommitmentsandcontingenciesNarrativeDetails" roleURI="http://www.healthequity.com/role/CommitmentsandcontingenciesNarrativeDetails">
        <link:definition>2435420 - Disclosure - Commitments and contingencies - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Indebtedness" roleURI="http://www.healthequity.com/role/Indebtedness">
        <link:definition>2136108 - Disclosure - Indebtedness</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IndebtednessTables" roleURI="http://www.healthequity.com/role/IndebtednessTables">
        <link:definition>2337308 - Disclosure - Indebtedness (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IndebtednessScheduleofLongtermDebtDetails" roleURI="http://www.healthequity.com/role/IndebtednessScheduleofLongtermDebtDetails">
        <link:definition>2438421 - Disclosure - Indebtedness - Schedule of Long-term Debt (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IndebtednessScheduleofLongtermDebtDetails_1" roleURI="http://www.healthequity.com/role/IndebtednessScheduleofLongtermDebtDetails_1">
        <link:definition>2438421 - Disclosure - Indebtedness - Schedule of Long-term Debt (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IndebtednessNarrativeDetails" roleURI="http://www.healthequity.com/role/IndebtednessNarrativeDetails">
        <link:definition>2439422 - Disclosure - Indebtedness - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Incometaxes" roleURI="http://www.healthequity.com/role/Incometaxes">
        <link:definition>2140109 - Disclosure - Income taxes</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncometaxesTables" roleURI="http://www.healthequity.com/role/IncometaxesTables">
        <link:definition>2341309 - Disclosure - Income taxes (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncometaxesComponentsofIncometaxDetails" roleURI="http://www.healthequity.com/role/IncometaxesComponentsofIncometaxDetails">
        <link:definition>2442423 - Disclosure - Income taxes - Components of Income tax (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncometaxesReconciliationofIncometaxDetails" roleURI="http://www.healthequity.com/role/IncometaxesReconciliationofIncometaxDetails">
        <link:definition>2443424 - Disclosure - Income taxes - Reconciliation of Income tax (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncometaxesNarrativeDetails" roleURI="http://www.healthequity.com/role/IncometaxesNarrativeDetails">
        <link:definition>2444425 - Disclosure - Income taxes - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncometaxesDeferredTaxAssetsandLiabilitiesDetails" roleURI="http://www.healthequity.com/role/IncometaxesDeferredTaxAssetsandLiabilitiesDetails">
        <link:definition>2445426 - Disclosure - Income taxes - Deferred Tax Assets and Liabilities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncometaxesUnrecognizedTaxBenefitsDetails" roleURI="http://www.healthequity.com/role/IncometaxesUnrecognizedTaxBenefitsDetails">
        <link:definition>2446427 - Disclosure - Income taxes - Unrecognized Tax Benefits (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Stockbasedcompensation" roleURI="http://www.healthequity.com/role/Stockbasedcompensation">
        <link:definition>2147110 - Disclosure - Stock-based compensation</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockbasedcompensationTables" roleURI="http://www.healthequity.com/role/StockbasedcompensationTables">
        <link:definition>2348310 - Disclosure - Stock-based compensation (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockbasedcompensationSummaryofShareBasedCompensationrecognizedDetails" roleURI="http://www.healthequity.com/role/StockbasedcompensationSummaryofShareBasedCompensationrecognizedDetails">
        <link:definition>2449428 - Disclosure - Stock-based compensation - Summary of Share Based Compensation recognized (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockbasedcompensationNarrativeDetails" roleURI="http://www.healthequity.com/role/StockbasedcompensationNarrativeDetails">
        <link:definition>2450429 - Disclosure - Stock-based compensation - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockbasedcompensationAssumptionsDetails" roleURI="http://www.healthequity.com/role/StockbasedcompensationAssumptionsDetails">
        <link:definition>2451430 - Disclosure - Stock-based compensation - Assumptions (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockbasedcompensationStockOptionActivityDetails" roleURI="http://www.healthequity.com/role/StockbasedcompensationStockOptionActivityDetails">
        <link:definition>2452431 - Disclosure - Stock-based compensation - Stock Option Activity (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockbasedcompensationRestrictedStockActivityDetails" roleURI="http://www.healthequity.com/role/StockbasedcompensationRestrictedStockActivityDetails">
        <link:definition>2453432 - Disclosure - Stock-based compensation - Restricted Stock Activity (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Fairvalue" roleURI="http://www.healthequity.com/role/Fairvalue">
        <link:definition>2154111 - Disclosure - Fair value</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FairvalueTables" roleURI="http://www.healthequity.com/role/FairvalueTables">
        <link:definition>2355311 - Disclosure - Fair value (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FairvalueNarrativeDetails" roleURI="http://www.healthequity.com/role/FairvalueNarrativeDetails">
        <link:definition>2456433 - Disclosure - Fair value - Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FairvalueDetails" roleURI="http://www.healthequity.com/role/FairvalueDetails">
        <link:definition>2457434 - Disclosure - Fair value (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Employeebenefits" roleURI="http://www.healthequity.com/role/Employeebenefits">
        <link:definition>2158112 - Disclosure - Employee benefits</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EmployeebenefitsDetails" roleURI="http://www.healthequity.com/role/EmployeebenefitsDetails">
        <link:definition>2459435 - Disclosure - Employee benefits (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Subsequentevents" roleURI="http://www.healthequity.com/role/Subsequentevents">
        <link:definition>2160113 - Disclosure - Subsequent events</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SubsequenteventsDetails" roleURI="http://www.healthequity.com/role/SubsequenteventsDetails">
        <link:definition>2461436 - Disclosure - Subsequent events (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
    </xs:appinfo>
  </xs:annotation>
  <xs:element id="hqy_UnrecognizedTaxBenefitsAmountNettedAgainstDeferredTaxAssets" abstract="false" name="UnrecognizedTaxBenefitsAmountNettedAgainstDeferredTaxAssets" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ShareBasedPaymentArrangementPlanModificationIncrementalCostNumberOfTeamMembers" abstract="false" name="ShareBasedPaymentArrangementPlanModificationIncrementalCostNumberOfTeamMembers" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:integerItemType"/>
  <xs:element id="hqy_CreditAgreementMember" abstract="true" name="CreditAgreementMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_EffectiveIncomeTaxRateReconciliationTaxCutsandJobsActof2017ChangeinDeferredTaxRate" abstract="false" name="EffectiveIncomeTaxRateReconciliationTaxCutsandJobsActof2017ChangeinDeferredTaxRate" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ComputerSoftwareAndCapitalizedSoftwareDevelopmentCostsMember" abstract="true" name="ComputerSoftwareAndCapitalizedSoftwareDevelopmentCostsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_DebtInstrumentAmortizationPeriodFiveMember" abstract="true" name="DebtInstrumentAmortizationPeriodFiveMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_SalesandMarketingMember" abstract="true" name="SalesandMarketingMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_SharebasedCompensationArrangementbySharebasedPaymentAwardAdditionalSharesAvailableforGrantsPercentageofCapitalStockOutstandingPercentage" abstract="false" name="SharebasedCompensationArrangementbySharebasedPaymentAwardAdditionalSharesAvailableforGrantsPercentageofCapitalStockOutstandingPercentage" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="hqy_SelfInsuranceMaximumCoveragePerIncident" abstract="false" name="SelfInsuranceMaximumCoveragePerIncident" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_EmployeeRelatedLiabilitiesCurrentMember" abstract="true" name="EmployeeRelatedLiabilitiesCurrentMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_EquityAwardsExchangedForCashInBusinessCombinationMember" abstract="true" name="EquityAwardsExchangedForCashInBusinessCombinationMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_DebtInstrumentPrepaymentCovenantPercentageOfProceedsFromSales" abstract="false" name="DebtInstrumentPrepaymentCovenantPercentageOfProceedsFromSales" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="hqy_UnionMesaMember" abstract="true" name="UnionMesaMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_InterestOnLongTermDebtToBePaid" abstract="false" name="InterestOnLongTermDebtToBePaid" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePriceRangeUpperRangeLimitOutstanding" abstract="false" name="ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePriceRangeUpperRangeLimitOutstanding" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="dtr-types:perShareItemType"/>
  <xs:element id="hqy_DisposalGroupIncludingDiscontinuedOperationOperatingLeaseRightOfUseAsset" abstract="false" name="DisposalGroupIncludingDiscontinuedOperationOperatingLeaseRightOfUseAsset" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_LossContingencyNumberOfLawsuits" abstract="false" name="LossContingencyNumberOfLawsuits" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:integerItemType"/>
  <xs:element id="hqy_InterestOnLongTermDebtToBePaidYearFour" abstract="false" name="InterestOnLongTermDebtToBePaidYearFour" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_AssetAcquisitionConsiderationToBePaid" abstract="false" name="AssetAcquisitionConsiderationToBePaid" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedClientHeldFundsObligation" abstract="false" name="BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedClientHeldFundsObligation" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_DebtInstrumentPrepaymentCovenantPeriodToReinvestProceedsFromSales" abstract="false" name="DebtInstrumentPrepaymentCovenantPeriodToReinvestProceedsFromSales" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="hqy_A401kCustomerRelationshipsMember" abstract="true" name="A401kCustomerRelationshipsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_EffectiveIncomeTaxRateReconciliationTaxExpenseBenefitEmployeeRemunerationPaymentsAmount" abstract="false" name="EffectiveIncomeTaxRateReconciliationTaxExpenseBenefitEmployeeRemunerationPaymentsAmount" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_BusinessCombinationProvisionalInformationInitialAccountingIncompleteAdjustmentClientHeldFundsObligation" abstract="false" name="BusinessCombinationProvisionalInformationInitialAccountingIncompleteAdjustmentClientHeldFundsObligation" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_DebtInstrumentCovenantNetLeverageRatio" abstract="false" name="DebtInstrumentCovenantNetLeverageRatio" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="xbrli:pureItemType"/>
  <xs:element id="hqy_StockIssuanceCostsPayable" abstract="false" name="StockIssuanceCostsPayable" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_DebtInstrumentPeriodicRepaymentsPercentageOfPrincipalAmount" abstract="false" name="DebtInstrumentPeriodicRepaymentsPercentageOfPrincipalAmount" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="hqy_AssetAcquisitionConsiderationToBePaidYearOne" abstract="false" name="AssetAcquisitionConsiderationToBePaidYearOne" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_IncreaseDecreaseInOperatingLeaseRightOfUseAsset" abstract="false" name="IncreaseDecreaseInOperatingLeaseRightOfUseAsset" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_AuditInformationAbstract" abstract="true" name="AuditInformationAbstract" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:stringItemType"/>
  <xs:element id="hqy_WageWorksInsurersMember" abstract="true" name="WageWorksInsurersMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_PerformanceRestrictedStockAwardsMember" abstract="true" name="PerformanceRestrictedStockAwardsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_AssetAcquisitionConsiderationToBePaidYearFour" abstract="false" name="AssetAcquisitionConsiderationToBePaidYearFour" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_TechnologyandDevelopmentMember" abstract="true" name="TechnologyandDevelopmentMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_AssetAcquisitionConsiderationToBePaidYearFive" abstract="false" name="AssetAcquisitionConsiderationToBePaidYearFive" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_AssetAcquisitionConsiderationToBePaidYearThree" abstract="false" name="AssetAcquisitionConsiderationToBePaidYearThree" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_LesseeOperatingLeaseNumberOfExtensions" abstract="false" name="LesseeOperatingLeaseNumberOfExtensions" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:integerItemType"/>
  <xs:element id="hqy_NonPassiveCustodialFundsMember" abstract="true" name="NonPassiveCustodialFundsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_DebtInstrumentPrepaymentCovenantPeriodToCommitToReinvestAfterInitialPeriod" abstract="false" name="DebtInstrumentPrepaymentCovenantPeriodToCommitToReinvestAfterInitialPeriod" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="hqy_AssetAcquisitionConsiderationAbstract" abstract="true" name="AssetAcquisitionConsiderationAbstract" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:stringItemType"/>
  <xs:element id="hqy_DebtInstrumentAmortizationPeriodOneMember" abstract="true" name="DebtInstrumentAmortizationPeriodOneMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePriceRangeUpperRangeLimitExercised" abstract="false" name="ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePriceRangeUpperRangeLimitExercised" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:perShareItemType"/>
  <xs:element id="hqy_AssetAcquisitionConsiderationToBePaidYearTwo" abstract="false" name="AssetAcquisitionConsiderationToBePaidYearTwo" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_A4500SeniorNotesDue2029Member" abstract="true" name="A4500SeniorNotesDue2029Member" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodRemainingModifiedRatio" abstract="false" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodRemainingModifiedRatio" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="hqy_OtherNonoperatingIncomeExpenseMiscellaneous" abstract="false" name="OtherNonoperatingIncomeExpenseMiscellaneous" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_PerformanceRestrictedStockUnitsMember" abstract="true" name="PerformanceRestrictedStockUnitsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_InterestOnLongTermDebtToBePaidAfterYearFive" abstract="false" name="InterestOnLongTermDebtToBePaidAfterYearFive" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_UnrecognizedTaxBenefitNet" abstract="false" name="UnrecognizedTaxBenefitNet" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_IncentivePlanMember" abstract="true" name="IncentivePlanMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_FurtherAcquisitionMember" abstract="true" name="FurtherAcquisitionMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_OtherAssetsPolicyTextBlock" abstract="false" name="OtherAssetsPolicyTextBlock" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:textBlockItemType"/>
  <xs:element id="hqy_DebtInstrumentAmortizationPeriodFourMember" abstract="true" name="DebtInstrumentAmortizationPeriodFourMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_InterestOnLongTermDebtToBePaidYearThree" abstract="false" name="InterestOnLongTermDebtToBePaidYearThree" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_PriorCreditAgreementMember" abstract="true" name="PriorCreditAgreementMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePriceRangeLowerRangeLimitOutstanding" abstract="false" name="ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePriceRangeLowerRangeLimitOutstanding" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="dtr-types:perShareItemType"/>
  <xs:element id="hqy_PaymentsToSettleClientHeldFunds" abstract="false" name="PaymentsToSettleClientHeldFunds" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_FollowOnEquityOfferingMember" abstract="true" name="FollowOnEquityOfferingMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_PaymentsForAssetAcquisition" abstract="false" name="PaymentsForAssetAcquisition" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_InterestOnLongTermDebtToBePaidYearOne" abstract="false" name="InterestOnLongTermDebtToBePaidYearOne" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ProceedsFromSaleOfOperatingLeaseRightOfUseAsset" abstract="false" name="ProceedsFromSaleOfOperatingLeaseRightOfUseAsset" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_AmortizationOfAcquiredIntangible" abstract="false" name="AmortizationOfAcquiredIntangible" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_TermLoanFacilityMember" abstract="true" name="TermLoanFacilityMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_DeferredTaxAssetsLeaseLiability" abstract="false" name="DeferredTaxAssetsLeaseLiability" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_DebtInstrumentAmortizationPeriodTwoAndThreePeriodMember" abstract="true" name="DebtInstrumentAmortizationPeriodTwoAndThreePeriodMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_WeightedAverageNumberOfSharesUsedInComputingNetIncomePerShareAttributableToCommonStockholdersBasicAndDilutedAbstract" abstract="true" name="WeightedAverageNumberOfSharesUsedInComputingNetIncomePerShareAttributableToCommonStockholdersBasicAndDilutedAbstract" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:stringItemType"/>
  <xs:element id="hqy_SubleaseIncomeToBeReceived" abstract="false" name="SubleaseIncomeToBeReceived" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_EffectiveIncomeTaxRateReconciliationNondeductibleExpenseAcquisitionRelatedCosts" abstract="false" name="EffectiveIncomeTaxRateReconciliationNondeductibleExpenseAcquisitionRelatedCosts" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ExpireInTaxYears2028Member" abstract="true" name="ExpireInTaxYears2028Member" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_TotalNonCashShareBasedPaymentArrangementExpenseMember" abstract="true" name="TotalNonCashShareBasedPaymentArrangementExpenseMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_PassiveCustodialFundsMember" abstract="true" name="PassiveCustodialFundsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_DebtInstrumentAmortizationPeriodDomain" abstract="true" name="DebtInstrumentAmortizationPeriodDomain" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_SharebasedCompensationArrangementbySharebasedPaymentAwardExpirationPeriodfromTerminationofEmployment" abstract="false" name="SharebasedCompensationArrangementbySharebasedPaymentAwardExpirationPeriodfromTerminationofEmployment" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="hqy_LuumAcquisitionMember" abstract="true" name="LuumAcquisitionMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_ContingentConsiderationMember" abstract="true" name="ContingentConsiderationMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_BusinessCombinationProvisionalInformationInitialAccountingIncompleteAdjustmentOtherCurrentAssets" abstract="false" name="BusinessCombinationProvisionalInformationInitialAccountingIncompleteAdjustmentOtherCurrentAssets" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_BusinessCombinationProvisionalInformationInitialAccountingIncompleteAdjustmentCashAndCashEquivalents" abstract="false" name="BusinessCombinationProvisionalInformationInitialAccountingIncompleteAdjustmentCashAndCashEquivalents" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_InterestOnLongTermDebtToBePaidYearTwo" abstract="false" name="InterestOnLongTermDebtToBePaidYearTwo" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_LesseeOperatingLeaseLeaseNotYetCommencedUndiscountedAmount" abstract="false" name="LesseeOperatingLeaseLeaseNotYetCommencedUndiscountedAmount" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ShareBasedPaymentArrangementDecreaseInExpenseDueToModificationOfTerms" abstract="false" name="ShareBasedPaymentArrangementDecreaseInExpenseDueToModificationOfTerms" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedAdjustmentCurrentLiabilitiesOther" abstract="false" name="BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedAdjustmentCurrentLiabilitiesOther" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_A401kMember" abstract="true" name="A401kMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_FurtherHealthSavingsAccountPortfolioAcquisitionMember" abstract="true" name="FurtherHealthSavingsAccountPortfolioAcquisitionMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePriceRangeLowerRangeLimitExercised" abstract="false" name="ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePriceRangeLowerRangeLimitExercised" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:perShareItemType"/>
  <xs:element id="hqy_AssetAcquisitionConsiderationToBePaidAfterYearFive" abstract="false" name="AssetAcquisitionConsiderationToBePaidAfterYearFive" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsRatio" abstract="false" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsRatio" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="hqy_InterestOnLongTermDebtToBePaidYearFive" abstract="false" name="InterestOnLongTermDebtToBePaidYearFive" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_BusinessCombinationRecognizedIdentifiableAssetsAcquiredandLiabilitiesAssumedOperatingLeaseRightofuseAssets" abstract="false" name="BusinessCombinationRecognizedIdentifiableAssetsAcquiredandLiabilitiesAssumedOperatingLeaseRightofuseAssets" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_EffectiveIncomeTaxRateReconciliationReclassificationOfOperatingLeaseRightOfUseAssets" abstract="false" name="EffectiveIncomeTaxRateReconciliationReclassificationOfOperatingLeaseRightOfUseAssets" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_WageWorksInc.Member" abstract="true" name="WageWorksInc.Member" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_InterestOnLongTermDebtFiscalYearMaturityAbstract" abstract="true" name="InterestOnLongTermDebtFiscalYearMaturityAbstract" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:stringItemType"/>
  <xs:element id="hqy_MergerIntegrationMember" abstract="true" name="MergerIntegrationMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_HSAMemberMember" abstract="true" name="HSAMemberMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_LesseeOperatingLeaseLiabilityToBePaidIncludingLeasesNotYetCommenced" abstract="false" name="LesseeOperatingLeaseLiabilityToBePaidIncludingLeasesNotYetCommenced" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_WageWorksIncMember" abstract="true" name="WageWorksIncMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_RACustomerRelationshipMember" abstract="true" name="RACustomerRelationshipMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_DebtInstrumentAmortizationPeriodAxis" abstract="true" name="DebtInstrumentAmortizationPeriodAxis" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrldt:dimensionItem" type="xbrli:stringItemType"/>
  <xs:element id="hqy_ScheduleofUnrecognizedTaxBenefitsNettedAgainstDeferredTaxAssetsTableTextBlock" abstract="false" name="ScheduleofUnrecognizedTaxBenefitsNettedAgainstDeferredTaxAssetsTableTextBlock" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:textBlockItemType"/>
  <xs:element id="hqy_MinimumNetWorthAboveCustodialAssets" abstract="false" name="MinimumNetWorthAboveCustodialAssets" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="hqy_LineOfCreditFacilityMaximumBorrowingCapacityOfFutureCommitments" abstract="false" name="LineOfCreditFacilityMaximumBorrowingCapacityOfFutureCommitments" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_BusinessCombinationProvisionalInformationInitialAccountingIncompleteAdjustmentDeferredIncomeTaxes" abstract="false" name="BusinessCombinationProvisionalInformationInitialAccountingIncompleteAdjustmentDeferredIncomeTaxes" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_DeferredTaxAssetsTaxCreditCarryforwardsResearchNoncurrent" abstract="false" name="DeferredTaxAssetsTaxCreditCarryforwardsResearchNoncurrent" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ExerciseOfStockOptionsReceivable" abstract="false" name="ExerciseOfStockOptionsReceivable" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_EffectiveIncomeTaxRateReconciliationChangeInNetOperatingLosses" abstract="false" name="EffectiveIncomeTaxRateReconciliationChangeInNetOperatingLosses" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_DeferredTaxLiabilitiesIncrementalContractCosts" abstract="false" name="DeferredTaxLiabilitiesIncrementalContractCosts" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_AcquiredHSAIntangibleAssetsMember" abstract="true" name="AcquiredHSAIntangibleAssetsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_IncreaseDecreaseInOperatingLeaseLiabilityNoncurrent" abstract="false" name="IncreaseDecreaseInOperatingLeaseLiabilityNoncurrent" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_ClientHeldFundsPolicyTextBlock" abstract="false" name="ClientHeldFundsPolicyTextBlock" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:textBlockItemType"/>
  <xs:element id="hqy_DebtInstrumentCovenantMinimumInterestCoverageRatio" abstract="false" name="DebtInstrumentCovenantMinimumInterestCoverageRatio" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="xbrli:pureItemType"/>
  <xs:element id="hqy_EffectiveIncomeTaxRateReconciliationReturnToProvisionAdjustments" abstract="false" name="EffectiveIncomeTaxRateReconciliationReturnToProvisionAdjustments" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="hqy_HealthSavingsAdministratorsLLCMember" abstract="true" name="HealthSavingsAdministratorsLLCMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="hqy_BusinessCombinationContingentConsiderationPerformancePeriod" abstract="false" name="BusinessCombinationContingentConsiderationPerformancePeriod" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="hqy_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodFairValue" abstract="false" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodFairValue" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
</xs:schema>
