First Amendment to Second Amended and Restated Refined Products Pipelines and Terminals Agreement entered into October 29, 2018, to be effective as of June 4, 2018, by and between HollyFrontier Refining & Marketing LLC, and Holly Energy Partners Operating, L.P

Exhibit 10.6

FIRST AMENDMENT

TO

SECOND AMENDED AND RESTATED

REFINED PRODUCT PIPELINES AND TERMINALS AGREEMENT

This First Amendment to Second Amended and Restated Refined Product Pipelines and Terminals Agreement (this “Amendment”) is dated as of October 29, 2018, to be effective as of June 4, 2018 (the “Effective Time”) by and between HOLLYFRONTIER REFINING & MARKETING LLC (“HFRM”) and HOLLY ENERGY PARTNERS-OPERATING, L.P. (“HEP Operating”). Each of HFRM and HEP Operating are collectively referred to herein as the “Parties.”

WHEREAS, the Parties desire to amend certain provisions of the Second Amended and Restated Refined Product Pipelines and Terminals Agreement, dated as of February 22, 2016, by and between HFRM and HEP Operating (the “Agreement”) as set forth herein.

NOW, THEREFORE, in consideration of the covenants and obligations contained herein, the Parties hereby agree as follows:

ARTICLE 1

AMENDMENTS

1.1 Section 2(n). Section 2(n) of the Agreement is hereby amended by deleting it in its entirety and replacing it with the following:

“Terminal Access Agreement. HFRM agrees to use its commercially reasonable efforts to enter into a terminal access agreement with any third party that uses any terminal owned by HEP Operating or its Affiliates where HFRM is the sole customer.

1.2 Amendment to Exhibit B. Exhibit B to the Agreement is hereby deleted and replaced in its entirety with Exhibit B attached to this Amendment.

1.3 Amendment to Exhibit C. Exhibit C to the Agreement is hereby deleted and replaced in its entirety with Exhibit C attached to this Amendment.

1.4 Amendment to Exhibit C-1. Exhibit C-1 to the Agreement is hereby deleted and replaced in its entirety with Exhibit C-1 attached to this Amendment.

ARTICLE 2

MISCELLANEOUS

2.1 Remainder of Agreement. Except as expressly set forth herein, this Amendment shall not by implication or otherwise alter, modify, amend or in any way affect any of the terms, conditions, obligations, covenants or agreements contained in the Agreement, all of which shall continue to be in full force and effect. Unless the context otherwise requires, after the execution and delivery hereof, any reference in the Agreement to “this Agreement” shall mean the Agreement as amended hereby.

2.2 Counterparts. This Amendment may be executed in counterparts each of which shall be deemed an original. An executed counterpart of this Amendment transmitted by facsimile shall be equally as effective as a manually executed counterpart.

2.3 Entire Agreement. The Agreement, as amended by this Amendment, contains the entire agreement between the Parties as to the subject matter of the Agreement and, except as provided for in this Amendment, the terms and provisions of the Agreement shall remain in full force and effect as originally written.

[Remainder of page intentionally left blank. Signature pages follow.]

IN WITNESS WHEREOF, the undersigned Parties have executed this Amendment as of the date first written above to be effective as of the Effective Time.

[Signature Page to First Amendment to Second Amended and Restated Refined Product Pipelines and Terminals Agreement]

EXHIBIT B

REFINED PRODUCT TERMINALS

As of February 1, 2016

EXHIBIT C

FEE SCHEDULE

As of July 1, 2018

EXHIBIT C-1

SCHEDULE OF ADDITIVE FEES