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<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

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    <periodOfReport>2020-04-02</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001481512</issuerCik>
        <issuerName>Ra Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>RARX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001688199</rptOwnerCik>
            <rptOwnerName>Read Simon</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RA PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>87 CAMBRIDGEPARK DRIVE</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02140</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
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            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Scientific Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

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            <transactionTimeliness>
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        <derivativeTransaction>
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            <expirationDate>
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                <value>Stock Option (Right to Buy)</value>
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                <directOrIndirectOwnership>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Restricted Stock Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
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            <transactionDate>
                <value>2020-04-02</value>
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    <footnotes>
        <footnote id="F1">Includes 6,361 shares of Issuer common stock acquired upon the vesting and net settlement of restricted stock units on February 1, 2020.</footnote>
        <footnote id="F2">Disposed of pursuant to an Agreement and Plan of Merger (the &quot;Merger Agreement&quot;), dated October 9, 2019, among Ra Pharmaceuticals, Inc. (the &quot;Issuer&quot;), UCB S.A., and Franq Merger Sub, Inc., providing for the merger (the &quot;Merger&quot;) of Franq Merger Sub, Inc. into the Issuer, in exchange for a cash payment of $48.00 per share.</footnote>
        <footnote id="F3">Pursuant to the Merger Agreement, at the effective time of the Merger, each option, whether vested or unvested, was cancelled in exchange for a cash payment equal to: (a) the number of shares of Issuer common stock underlying the option, multiplied by (b) the excess of $48.00 over the per share exercise price of such option.</footnote>
        <footnote id="F4">Pursuant to the Merger Agreement, at the effective time of the Merger, each restricted stock unit was canceled in exchange for a cash payment equal to $48.00 per share underlying each restricted stock unit.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ David C. Lubner, Attorney-in Fact for Simon Read</signatureName>
        <signatureDate>2020-04-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
