<PAGE>

EXHIBIT 10.25


     THIS FIRST SUPPLEMENTAL INDENTURE, dated as of January 13, 2000, among
PACER INTERNATIONAL, INC., a Tennessee corporation (the "Company"), CONEX
                                                         -------
ACQUISITION CORPORATION, a Delaware corporation ("Newco"), and Wilmington Trust
                                                  -----
Company, as trustee (the "Trustee"), under the Indenture (referred to
                          -------
hereinafter) pursuant to which the Company issued its 11 3/4% Senior
Subordinated Notes due 2007 (the "Securities").
                                  ----------

                                  WITNESSETH:

WHEREAS, the Company, the Guarantors named therein, and the Trustee executed and
delivered a certain Indenture dated as of May 28, 1999 (the "Indenture"),
                                                             ---------
providing for the issuance of up to an aggregate principal amount of
$150,000,000 of the Securities;

WHEREAS, the Company by appropriate action has determined that it is desirable
to amend certain provisions of the Indenture; and

WHEREAS, pursuant to a Subscription Agreement dated January 13, 2000, the
Company is acquiring the capital stock of Newco; and

WHEREAS, Section 4.18 of the Indenture provides that under certain circumstances
the Company is required to cause Domestic Restricted Subsidiaries which are not
Guarantors to execute and deliver to the Trustee a supplemental indenture and
Guarantee (as defined in the Indenture) pursuant to which such Domestic
Restricted Subsidiaries shall unconditionally guarantee all of the Company's
obligations under the Securities and the Indenture on the terms set forth in the
Indenture; and

NOW THEREFORE, in consideration of the foregoing and for other good and valuable
consideration, the receipt of which is hereby acknowledged, Newco, the Company
and the Trustee mutually covenant and agree for the equal and ratable benefit of
the holders of the Securities as set forth below.


                                   Article I

                                   Amendment

     1.1  Newco hereby, jointly and severally with all other Guarantors,
unconditionally and irrevocably guarantees, on a senior subordinated basis, the
Company's obligations under the Indenture and the Securities on the terms and
subject to the conditions set forth in Article Eleven of the Indenture.

     1.2  Except as expressly amended hereby, the Indenture is in all respects
ratified and confirmed and all the terms, conditions and provisions thereof
shall remain in full force and effect.  This First Supplemental Indenture shall
form a part of the Indenture for all purposes, and every holder of Securities
heretofore or hereafter authenticated and delivered shall be bound hereby.
<PAGE>

                           Miscellaneous Provisions

     1.3  For all purposes of this First Supplemental Indenture, except as
otherwise defined or unless the context otherwise requires, capitalized terms
used herein and not defined herein shall have the meaning specified in the
Indenture.

     1.4  THIS FIRST SUPPLEMENTAL INDENTURE WILL BE GOVERNED BY AND CONSTRUED IN
ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK, AS APPLIED TO CONTRACTS MADE
AND PERFORMED WITHIN THE STATE OF NEW YORK, WITHOUT REGARD TO PRINCIPLES OF
CONFLICTS OF LAW.

     1.5  All provisions in this First Supplemental Indenture respecting the
Company shall bind or inure to the benefit of (as the case may be) the Company,
its successors or assigns.

     1.6  The recitals contained herein shall be taken as the statements of the
Company and Newco and the Trustee assumes no responsibility for their
correctness.  The Trustee makes no representations as to the validity of this
First Supplemental Indenture.

     1.7  This First Supplemental Indenture may be executed in any number of
counterparts, each of which shall be an original, but such counterparts shall
together constitute but one and the same instrument.

                                    ********
<PAGE>

IN WITNESS WHEREOF, the parties hereto have caused this First Supplemental
Indenture to be duly executed as of the date first above written.


                              PACER INTERNATIONAL, INC.

                              By:
                                  --------------------------------------
                              Name:  Lawrence C. Yarberry
                              Title: Executive Vice President and Chief
                                     Financial Officer


                              CONEX ACQUISITION CORPORATION,
                              as Guarantor

                              By:
                                  --------------------------------------
                              Name:  Lawrence C. Yarberry
                              Title: Secretary and Treasurer


                              WILMINGTON TRUST COMPANY,
                              as Trustee

                              By:
                                  --------------------------------------
                              Name:
                              Title: