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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-10-31</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001297709</rptOwnerCik>
            <rptOwnerName>Novartis Bioventures Ltd</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O NOVARTIS INTERNATIONAL AG</rptOwnerStreet1>
            <rptOwnerStreet2>WSJ-200.220</rptOwnerStreet2>
            <rptOwnerCity>CH-4002 BASEL</rptOwnerCity>
            <rptOwnerState>V8</rptOwnerState>
            <rptOwnerZipCode>0000000000</rptOwnerZipCode>
            <rptOwnerStateDescription>SWITZERLAND</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001114448</rptOwnerCik>
            <rptOwnerName>NOVARTIS AG</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>LICHTSTRASSE 35</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BASEL</rptOwnerCity>
            <rptOwnerState>V8</rptOwnerState>
            <rptOwnerZipCode>CH 4056</rptOwnerZipCode>
            <rptOwnerStateDescription>SWITZERLAND</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>2016-10-31</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>X</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>62914</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.07</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
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                </transactionAcquiredDisposedCode>
            </transactionAmounts>
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                    <value>62914</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
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                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2016-10-31</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
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                <footnoteId id="F2"/>
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            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>339</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>13.00</value>
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                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
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                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>62575</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
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        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
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            <transactionDate>
                <value>2016-10-31</value>
            </transactionDate>
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                <value></value>
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            <transactionAmounts>
                <transactionShares>
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                <transactionPricePerShare>
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                <transactionAcquiredDisposedCode>
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                    <value>1452372</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
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                    <value>D</value>
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        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
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            <transactionDate>
                <value>2016-10-31</value>
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            <transactionCoding>
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            <transactionTimeliness>
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            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1974933</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
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            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2016-10-31</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>486104</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F5"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2461037</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
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            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2016-10-31</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>84615</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>13.00</value>
                </transactionPricePerShare>
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                </transactionAcquiredDisposedCode>
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            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2545652</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
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            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrants to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.07</value>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-10-31</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>X</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>62914</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2022-04-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>62914</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
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                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
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                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Series A Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-10-31</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
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            <transactionAmounts>
                <transactionShares>
                    <value>9728589</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1389797</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
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                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Series B-1 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-10-31</value>
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            <transactionCoding>
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                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>3657932</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>522561</value>
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            </underlyingSecurity>
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                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Series B-2 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F5"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-10-31</value>
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                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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                <value></value>
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                <transactionShares>
                    <value>3402729</value>
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                <transactionPricePerShare>
                    <footnoteId id="F5"/>
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                <transactionAcquiredDisposedCode>
                    <value>D</value>
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            <exerciseDate>
                <footnoteId id="F5"/>
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            <expirationDate>
                <footnoteId id="F5"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>486104</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
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        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The board of directors of Novartis Bioventures Ltd. has sole voting and investment control and power over such securities. None of the members of its board of directors has individual voting or investment power with respect to such securities and each disclaims beneficial ownership of such securities. Novartis Bioventures Ltd. is an indirectly owned subsidiary of Novartis AG.</footnote>
        <footnote id="F2">The Warrants automatically exercised immediately prior to the closing of the Issuer's initial public offering for such number of shares issuable pursuant to a cashless net exercise provision, resulting in the Issuer withholding 339 of the warrant shares to pay the exercise price and issuing to the reporting person the remaining 62,575 shares, after deducting the aggregate exercise price.</footnote>
        <footnote id="F3">Each share of the Series A Preferred Stock is convertible into Common Stock on a 1-for-7 basis automatically upon the closing of the Issuer's initial public offering, and has no expiration date.</footnote>
        <footnote id="F4">Each share of the Series B-1 Preferred Stock is convertible into Common Stock on a 1-for-7 basis automatically upon the closing of the Issuer's initial public offering, and has no expiration date.</footnote>
        <footnote id="F5">Each share of the Series B-2 Preferred Stock is convertible into Common Stock on a 1-for-7 basis automatically upon the closing of the Issuer's initial public offering, and has no expiration date.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Simon Zivi, Authorized Signatory /s/ Laurieann Chaikowsky, Authorized Signatory</signatureName>
        <signatureDate>2016-10-31</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Simon Zivi, Chairman /s/ Laurieann Chaikowsky, Authorized Signatory</signatureName>
        <signatureDate>2016-10-31</signatureDate>
    </ownerSignature>
</ownershipDocument>
