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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2019-06-11</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001619841</rptOwnerCik>
            <rptOwnerName>Shah Rajeev M.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RA CAPITAL MANAGEMENT, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>20 PARK PLAZA, SUITE 1200</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>19.88</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2019-06-11</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>15000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2029-06-11</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>15000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>15000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">On June 11, 2019, the Reporting Person was granted an option to purchase 15,000 shares of Common Stock. The option shall vest and become exercisable in a single annual installment upon the earlier of (i) the first anniversary of the grant date of June 11, 2019 or (ii) the Issuer's annual meeting of shareholders in 2020.</footnote>
        <footnote id="F2">Under the Reporting Person's arrangement with RA Capital Management, LLC (the &quot;Manager&quot;), the Reporting Person holds the option for the benefit of RA Capital Healthcare Fund, L.P. (the &quot;Fund&quot;) and a separately managed account (the &quot;Account&quot;). The Reporting Person is obligated to turn over to the Manager any net cash or stock received upon exercise of the option, which will offset advisory fees owed by the Fund and Account to the Manager. The Reporting Person therefore disclaims beneficial ownership of the option and underlying common stock.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ David C. Lubner, Attorney-in-fact for Rajeev M. Shah</signatureName>
        <signatureDate>2019-06-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
