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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2007-09-18</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000934612</issuerCik>
        <issuerName>BURLINGTON NORTHERN SANTA FE CORP</issuerName>
        <issuerTradingSymbol>BNI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001067983</rptOwnerCik>
            <rptOwnerName>BERKSHIRE HATHAWAY INC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1440 KIEWIT PLAZA</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>OMAHA</rptOwnerCity>
            <rptOwnerState>NE</rptOwnerState>
            <rptOwnerZipCode>68131</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000315090</rptOwnerCik>
            <rptOwnerName>BUFFETT WARREN E</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1440 KIEWIT PLAZA</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>OMAHA</rptOwnerCity>
            <rptOwnerState>NE</rptOwnerState>
            <rptOwnerZipCode>68131</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000109694</rptOwnerCik>
            <rptOwnerName>OBH INC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1440 KIEWIT PLAZA</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>OMAHA</rptOwnerCity>
            <rptOwnerState>NE</rptOwnerState>
            <rptOwnerZipCode>68131</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>52975000</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes 1 and 2</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Call option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>40.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2007-09-18</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>392378</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>39.10</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2007-10-03</value>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2007-10-03</value>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>392378</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>7847818</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F4"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote 4</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These shares are owned by the following subsidiaries of Berkshire Hathaway Inc.: National Indemnity Company (&quot;NICO&quot;) (26,951,000 shares); National Fire &amp; Marine Insurance Company (&quot;NFMIC&quot;) (1,322,100 shares); and Columbia Insurance Company (&quot;Columbia&quot;) (24,701,900 shares).  Each of NICO, NFMIC and Columbia is a subsidiary of OBH, Inc. (&quot;OBH&quot;).  OBH is a subsidiary of Berkshire Hathaway Inc. (&quot;Berkshire&quot;).</footnote>
        <footnote id="F2">As OBH and Berkshire are each in the chain of ownership of NICO, NFMIC and Columbia, each of Berkshire and OBH may be deemed presently to both beneficially own and have a pecuniary interest in all shares of Burlington Northern common stock presently owned by each subsidiary.  Warren E. Buffett, as the controlling stockholder of Berkshire, may be deemed presently to beneficially own, but only to the extent he has a pecuniary interest in, the shares of Burlington Northern common stock presently owned by each such subsidiary.  Mr. Buffett disclaims beneficial ownership of the reported securities except to the extent of his pecuniary interest therein.</footnote>
        <footnote id="F3">The exercise date and expiration date may be extended to November 2, 2007 for an additional premium to be determined on October 3, 2007.</footnote>
        <footnote id="F4">The call options are held by National Indemnity Company.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Berkshire Hathaway Inc., by Marc D. Hamburg</signatureName>
        <signatureDate>2007-09-20</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Warren E. Buffett</signatureName>
        <signatureDate>2007-09-20</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>OBH, Inc., by Marc D. Hamburg</signatureName>
        <signatureDate>2007-09-20</signatureDate>
    </ownerSignature>
</ownershipDocument>
