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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2011-04-13</periodOfReport>

    <dateOfOriginalSubmission>2011-04-15</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001390478</issuerCik>
        <issuerName>RXI PHARMACEUTICALS CORP</issuerName>
        <issuerTradingSymbol>RXII</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001297696</rptOwnerCik>
            <rptOwnerName>Hillsberg Sanford</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O RXI PHARMACEUTICALS CORPORATION</rptOwnerStreet1>
            <rptOwnerStreet2>60 PRESCOTT STREET</rptOwnerStreet2>
            <rptOwnerCity>WORCESTER</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>01605</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2011-04-13</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>120838</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>126838</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The number of shares initally report to have been received pursuant to the Merger was incorrect.</footnote>
        <footnote id="F2">Received in exchange for 993,739 shares of Apthera, Inc. common stock in connection with merger of Apthers, Inc. into RXI Pharmaceuticals Corporation (the &quot;Merger&quot;). On the effective date of the Merger, the closing price of RXI Pharmaceuticals Corporation common stock was $1.275 per share.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/Marc A. Rubenstein, Attorney-in-Fact</signatureName>
        <signatureDate>2011-04-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
