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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-08-18</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001283140</issuerCik>
        <issuerName>HOLLY ENERGY PARTNERS LP</issuerName>
        <issuerTradingSymbol>HEP</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000048039</rptOwnerCik>
            <rptOwnerName>HOLLY CORP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>100 CRESCENT COURT</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 1600</rptOwnerStreet2>
            <rptOwnerCity>DALLAS</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>75201</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>Please see remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001296165</rptOwnerCik>
            <rptOwnerName>Navajo Pipeline Co., L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>100 CRESCENT COURT</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 1600</rptOwnerStreet2>
            <rptOwnerCity>DALLAS</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>75201</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001296169</rptOwnerCik>
            <rptOwnerName>HEP Logistics Holdings, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>100 CRESCENT COURT</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 1600</rptOwnerStreet2>
            <rptOwnerCity>DALLAS</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>75201</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001296166</rptOwnerCik>
            <rptOwnerName>Holly Logistic Services, L.L.C.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>100 CRESCENT COURT</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 1600</rptOwnerStreet2>
            <rptOwnerCity>DALLAS</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>75201</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Units</value>
            </securityTitle>
            <transactionDate>
                <value>2009-08-18</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>7000000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>7217497</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Units</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>72503</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Subordinated Units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2009-08-18</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>7000000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F7"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F6"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Units</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>7000000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F7"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F7"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The transaction described herein is also exempt under Rule 16(b)-6(b) as the conversion of a derivative security, thus Transaction Code C is also applicable.</footnote>
        <footnote id="F2">7,000,000 Subordinated Units converted into an equal number of Common Units on August 18, 2009 pursuant to the terms of the Issuer's First Amended and Restated Agreement of Limited Partnership dated as of July 13, 2004, as amended.</footnote>
        <footnote id="F3">These common units are owned by Navajo Pipeline Co., L.P. (&quot;NPC&quot;), Navajo Refining Company, L.L.C. (&quot;NRC&quot;), Woods Cross Refining Company, L.L.C. (&quot;WX&quot;) and HEP Logistics Holdings, L.P. (&quot;GP LP&quot;).  These common units are held 127,440 by NPC, 59,844 by NRC, 30,213 by WX and 7,000,000 by GP LP.</footnote>
        <footnote id="F4">1-for-1.</footnote>
        <footnote id="F5">Immediately.</footnote>
        <footnote id="F6">None.</footnote>
        <footnote id="F7">N/A</footnote>
    </footnotes>

    <remarks>Holly Corporation indirectly owns 100% of each NPC, NRC and WX. NPC is the sole member of Holly Logistic Services, L.L.C. (&quot;GP LLC&quot;) and the sole limited partner of GP LP. GP LLC is the sole general partner of GP LP. GP LP is the sole general partner of the Issuer. The joint filers are jointly filing this Form 4 and information regarding the joint filers, other than Holly Corporation, is set forth on Exhibit 99 to this Form 4. The reporting persons disclaim beneficial ownership of the reported securities except to the extent of their pecuniary interests therein, and this report shall not be deemed an admission that the reporting persons are beneficial owners of the reported securities for purposes of Section 16 or for any other purpose.</remarks>

    <ownerSignature>
        <signatureName>Bruce R. Shaw, Senior Vice President and Chief Financial Officer</signatureName>
        <signatureDate>2009-08-19</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By: Navajo Pipeline GP, L.L.C., its General Partner / by: Bruce R. Shaw, Vice President and Chief Financial Officer</signatureName>
        <signatureDate>2009-08-18</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By: Holly Logistic Services, L.L.C., its General Partner / By Bruce R. Shaw, Sr.VP and CFO</signatureName>
        <signatureDate>2009-08-18</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Bruce R. Shaw, Senior Vice President and Chief Financial Officer</signatureName>
        <signatureDate>2009-08-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
