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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2020-02-24</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001269021</issuerCik>
        <issuerName>PORTOLA PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>PTLA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001564621</rptOwnerCik>
            <rptOwnerName>Moriarty John B</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O PORTOLA PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>270 E. GRAND AVE.</rptOwnerStreet2>
            <rptOwnerCity>SOUTH SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94080</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>EVP, General Counsel</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Performance Stock Unit</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2020-02-24</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>73125</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2023-02-24</value>
                <footnoteId id="F5"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>73125</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>73125</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Each performance stock unit (PSU) represents a contingent right to receive one (1) share of the Issuer's common stock.</footnote>
        <footnote id="F2">One-third of the PSUs will be earned one or after the one (1) year anniversary of the grant date of February 24, 2020 and when the average closing price of the Issuer's Common Stock on the Nasdaq Global Select Market appreciates 50% per share from the grant date closing price of Issuer's Common Stock on the Nasdaq Global Market over a period of twenty (20) consecutive trading days. The closing price of the Issuer's Common Stock on the Nasdaq Global Market on February 24, 2020 was $13.06.</footnote>
        <footnote id="F3">One-third of the PSUs will be earned on or after the two (2) year anniversary of the grant date of February 24, 2020 and when the average closing price of the Issuer's Common Stock on the Nasdaq Global Select Market appreciates 100% per share from the grant date closing price of the Issuer's Common Stock on the Nasdaq Global Select Market over a period of twenty (20) consecutive trading days. The closing price of the Issuer's Common Stock on the Nasdaq Global Market on February 24, 2020 was $13.06.</footnote>
        <footnote id="F4">One-third of the PSUs will be earned on the three (3) year anniversary of the grant date of February 24, 2020 and when the average closing price of the Issuer's Common Stock on the Nasdaq Global Select Market appreciates 150% per share from the grant date closing price of the Issuer's Common Stock on the Nasdaq Global Select Market over a period of twenty (2) consecutive trading days. The closing price of the Issuer's Common Stock on the Nasdaq Global Market on February 24, 2020 was $13.06.</footnote>
        <footnote id="F5">Any PSUs not yearned on the three (3) year anniversary of the grant date will expire.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Mike Ouimette, as attorney-in-fact</signatureName>
        <signatureDate>2020-02-26</signatureDate>
    </ownerSignature>
</ownershipDocument>
