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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2020-08-06</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001651431</issuerCik>
        <issuerName>Checkmate Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>CMPI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001202793</rptOwnerCik>
            <rptOwnerName>POWELL MICHAEL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SOFINNOVA INVESTMENTS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3000 SAND HILL ROAD, BLDG. 4, SUITE 250</rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001612133</rptOwnerCik>
            <rptOwnerName>Sofinnova Venture Partners IX, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SOFINNOVA INVESTMENTS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3000 SAND HILL ROAD, BLDG. 4, SUITE 250</rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001612134</rptOwnerCik>
            <rptOwnerName>Sofinnova Management IX, L.L.C.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SOFINNOVA INVESTMENTS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3000 SAND HILL ROAD, BLDG. 4, SUITE 250</rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001245624</rptOwnerCik>
            <rptOwnerName>HEALY JAMES</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SOFINNOVA INVESTMENTS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3000 SAND HILL ROAD, BLDG. 4, SUITE 250</rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1671771</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1314165</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>487438</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The Series A Preferred Stock and Series C Preferred Stock is convertible into Common Stock at a rate of 1:7.4771 into the number of shares of Common Stock as shown in Column 3 at any time at the holder's election, and automatically upon the closing of the Issuer's initial public offering without payment or further consideration. The shares have no expiration date.</footnote>
        <footnote id="F2">The Series B Preferred Stock is convertible into Common Stock at a rate of 1.12256:7.4771 into the number of shares of Common Stock as shown in Column 3 at any time at the holder's election, and automatically upon the closing of the Issuer's initial public offering without payment or further consideration. The shares have no expiration date.</footnote>
        <footnote id="F3">The shares are held directly by Sofinnova Venture Partners IX, L.P. (the &quot;Fund&quot;). The general partner of the Fund is Sofinnova Management IX, L.L.C. (the &quot;GP&quot;) and may be deemed to have sole voting, investment and dispositive power with respect to the securities held by the Fund. Dr. James I. Healy and Michael F. Powell, Ph.D. are the managing members of the GP and may be deemed to have shared voting, investment and dispositive power with respect to the securities held by the Fund. Each reporting person disclaims beneficial ownership of such securities, except to the extent of his or its proportionate pecuniary interest therein, if any.</footnote>
    </footnotes>

    <remarks>Exhibit 24 - Power of Attorney</remarks>

    <ownerSignature>
        <signatureName>/s/ Nathalie Auber, attorney-in-fact for Sofinnova Venture Partners IX, L.P.</signatureName>
        <signatureDate>2020-08-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Nathalie Auber, attorney-in-fact for Sofinnova Management IX, L.L.C..</signatureName>
        <signatureDate>2020-08-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Nathalie Auber, attorney-in-fact for James I Healy</signatureName>
        <signatureDate>2020-08-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Nathalie Auber, attorney-in-fact for Michael F. Powell</signatureName>
        <signatureDate>2020-08-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
