<?xml version="1.0" encoding="utf-8"?>
<!--Generated by DFIN XBRL Instance Document - http://www.dfinsolutions.com/ - Version R3.0 - on 23-June-2025 [10:05:39] {AM}-->
<schema targetNamespace="http://wave.com/20241231" elementFormDefault="qualified" xmlns:wve="http://wave.com/20241231" xmlns="http://www.w3.org/2001/XMLSchema" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xl="http://www.xbrl.org/2003/XLink" xmlns:us-gaap="http://fasb.org/us-gaap/2024" xmlns:country="http://xbrl.sec.gov/country/2024" xmlns:dei="http://xbrl.sec.gov/dei/2024" xmlns:us-types="http://fasb.org/us-types/2024" xmlns:deprecated="http://www.xbrl.org/2009/arcrole/fact-explanatoryFact" xmlns:srt="http://fasb.org/srt/2024" xmlns:srt-types="http://fasb.org/srt-types/2024" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2020-01-21" xmlns:ecd="http://xbrl.sec.gov/ecd/2024">
  <annotation>
    <appinfo>
      <link:linkbase id="lnk" >
        <link:roleRef xlink:type="simple" xlink:href="https://xbrl.sec.gov/ecd/2024/ecd-2024.xsd#PvpDisclosure" roleURI="http://xbrl.sec.gov/ecd/role/PvpDisclosure"  />
        <link:roleRef xlink:type="simple" xlink:href="https://xbrl.sec.gov/ecd/2024/ecd-2024.xsd#PvpAdjustmentsOnly" roleURI="http://xbrl.sec.gov/ecd/role/PvpAdjustmentsOnly"  />
        <link:roleRef xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedLabel" roleURI="http://www.xbrl.org/2009/role/negatedLabel"  />
        <link:roleRef xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedPeriodEndLabel" roleURI="http://www.xbrl.org/2009/role/negatedPeriodEndLabel"  />
        <link:roleRef xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedPeriodStartLabel" roleURI="http://www.xbrl.org/2009/role/negatedPeriodStartLabel"  />
        <link:roleRef xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedTotalLabel" roleURI="http://www.xbrl.org/2009/role/negatedTotalLabel"  />
        <link:roleRef xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedNetLabel" roleURI="http://www.xbrl.org/2009/role/negatedNetLabel"  />
        <link:roleRef xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedTerseLabel" roleURI="http://www.xbrl.org/2009/role/negatedTerseLabel"  />
        <link:roleRef xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/net-2009-12-16.xsd#netLabel" roleURI="http://www.xbrl.org/2009/role/netLabel"  />
        <link:presentationLink xlink:type="extended" xlink:role="http://xbrl.sec.gov/ecd/role/PvpDisclosure" >
          <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/ecd/2024/ecd-2024.xsd#ecd_AllAdjToCompMember" xlink:label="loc_ecd_AllAdjToCompMember_120167019" />
          <link:loc xlink:type="locator" xlink:href="wve-20241231.xsd#wve_StockandOptionAwardsMember" xlink:label="loc_WVE_StockandOptionAwardsMember_120167010" />
          <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_ecd_AllAdjToCompMember_120167019" xlink:to="loc_WVE_StockandOptionAwardsMember_120167010" order="100" preferredLabel="http://www.xbrl.org/2003/role/label" />
        </link:presentationLink>
        <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/all" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all"  />
        <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-default"  />
        <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-domain"  />
        <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/domain-member" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#domain-member"  />
        <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#hypercube-dimension"  />
        <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/notAll" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#notAll"  />
        <link:definitionLink xlink:type="extended" xlink:role="http://xbrl.sec.gov/ecd/role/PvpAdjustmentsOnly" >
          <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/ecd/2024/ecd-2024.xsd#ecd_AllAdjToCompMember" xlink:label="loc_ecd_AllAdjToCompMember_120167019" />
          <link:loc xlink:type="locator" xlink:href="wve-20241231.xsd#wve_StockandOptionAwardsMember" xlink:label="loc_WVE_StockandOptionAwardsMember_120167010" />
          <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_ecd_AllAdjToCompMember_120167019" xlink:to="loc_WVE_StockandOptionAwardsMember_120167010" order="100" />
        </link:definitionLink>
        <link:labelLink xlink:type="extended" xlink:role="http://www.xbrl.org/2003/role/link" >
          <link:loc xlink:type="locator" xlink:href="wve-20241231.xsd#wve_StockandOptionAwardsMember" xlink:label="loc_wve_StockandOptionAwardsMember" />
          <link:label xlink:type="resource" xlink:role="http://www.xbrl.org/2003/role/label" xlink:label="lab_wve_StockandOptionAwardsMember" xml:lang="en-US">Stock and Option Awards [Member]</link:label>
          <link:labelArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/concept-label" xlink:from="loc_wve_StockandOptionAwardsMember" xlink:to="lab_wve_StockandOptionAwardsMember" />
        </link:labelLink>
      </link:linkbase>
    </appinfo>
  </annotation>
  <import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd" />
  <import namespace="http://www.xbrl.org/2003/linkbase" schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" />
  <import namespace="http://xbrl.sec.gov/dei/2024" schemaLocation="https://xbrl.sec.gov/dei/2024/dei-2024.xsd" />
  <import namespace="http://xbrl.sec.gov/dei-sub/2024" schemaLocation="https://xbrl.sec.gov/dei/2024/dei-sub-2024.xsd" />
  <import namespace="http://www.xbrl.org/dtr/type/2020-01-21" schemaLocation="https://www.xbrl.org/dtr/type/2020-01-21/types.xsd" />
  <import namespace="http://fasb.org/srt/2024" schemaLocation="https://xbrl.fasb.org/srt/2024/elts/srt-2024.xsd" />
  <import namespace="http://fasb.org/srt-types/2024" schemaLocation="https://xbrl.fasb.org/srt/2024/elts/srt-types-2024.xsd" />
  <import namespace="http://xbrl.sec.gov/ecd-sub/2024" schemaLocation="https://xbrl.sec.gov/ecd/2024/ecd-sub-2024.xsd" />
  <import namespace="http://xbrl.sec.gov/ecd/2024" schemaLocation="https://xbrl.sec.gov/ecd/2024/ecd-2024.xsd" />
  <import namespace="http://www.xbrl.org/2006/ref" schemaLocation="http://www.xbrl.org/2006/ref-2006-02-27.xsd" />
  <import namespace="http://xbrl.org/2005/xbrldt" schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd" />
  <import namespace="http://fasb.org/srt-roles/2024" schemaLocation="https://xbrl.fasb.org/srt/2024/elts/srt-roles-2024.xsd" />
  <element name="StockandOptionAwardsMember" type="dtr-types:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" id="wve_StockandOptionAwardsMember" substitutionGroup="xbrli:item" />
</schema>
