<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2021-06-28</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001623526</issuerCik>
        <issuerName>Stoke Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>STOK</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001593440</rptOwnerCik>
            <rptOwnerName>ATP Life Science Ventures, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O APPLE TREE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>230 PARK AVENUE, 28TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10169</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001593453</rptOwnerCik>
            <rptOwnerName>ATP III GP, Ltd.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O APPLE TREE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>230 PARK AVENUE, 28TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10169</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2021-06-28</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>17161713</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The shares were distributed in a pro rata distribution to the limited partners of ATP Life Science Ventures, L.P. (&quot;ATP,&quot; and formerly known as Apple Tree Partners IV, L.P.).</footnote>
        <footnote id="F2">The shares were directly held by ATP. ATP III GP, Ltd. (&quot;ATP GP&quot;) is the sole general partner of ATP. Seth L. Harrison is a director on the Issuer's board of directors and is the sole director of ATP GP. ATP GP and Dr. Harrison disclaim beneficial ownership of the reported shares, except to the extent of any pecuniary interest therein.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Seth L. Harrison, for ATP Life Science Ventures, L.P., By: Seth L. Harrison, as director of ATP III GP, Ltd., its general partner</signatureName>
        <signatureDate>2021-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Seth L. Harrison, for ATP III GP, Ltd., By: Seth L. Harrison, director</signatureName>
        <signatureDate>2021-06-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
