Document:

<PAGE>

                                                                  Exhibit 10.38

                               FIRST AMENDMENT TO
                            PACER INTERNATIONAL, INC.
                             1999 STOCK OPTION PLAN

FIRST AMENDMENT TO PACER INTERNATIONAL, INC. 1999 STOCK OPTION PLAN dated as of
September 9, 2000.

     1. Section 2 of the Pacer International, Inc. 1999 Stock Option Plan (the
"Plan") is amended as to the definitions set forth below and restated as to
the definitions set forth below to read as follows:

          "Anniversary Date" means each of the successive annual anniversary
     dates of the Effective Date, with the first Anniversary Date being May 28,
     2000.

          "Effective Date" means the date of consummation of the transactions
     contemplated under the Merger Agreement and under the Stock Purchase
     Agreement, which is May 28, 1999.

          "Tranche A Options" has the meaning set forth in Section 4(e).

          "Tranche B Options" has the meaning set forth in Section 4(e).

          "Tranche C Options" has the meaning set forth in Section 4(e).

     2. Section 6(a) of the Plan is amended in its entirety and restated to read
as follows:

          Section 6(a). Vesting Schedule. Tranche A Options granted to an
     Optionee shall become Vested Options in five equal installments on each of
     the first five Anniversary Dates following the issuance of the Tranche A
     Options to the Optionee, provided the Optionee is employed by the Company
     on each such Anniversary Date.

     3. Section 7(a) of the Plan is amended in its entirety and restated to read
as follows:

          Section 7(a). Vesting Schedule. All of the Tranche B Options granted
     to an Optionee on a particular date (the "Tranche B Grant Date") shall
     become Vested Options on the date that is seven years immediately following
     the Tranche B Grant Date ("Tranche B Vesting Date") if the Optionee is
     employed by the Company on the Tranche B Vesting Date.

<PAGE>

          However, if the Per Share Equity Value as of any of the first five
     Tranche B Performance Measurement Dates following the Tranche B Grant Date
     as indicated below (each a "Tranche B Performance Measurement Date") equals
     or exceeds the corresponding Tranche B Per Share Target Value indicated
     below for such date (the "Tranche B Per Share Target Value"), then 20% of
     the Tranche B Options issued to such Optionee on such Tranche B Grant Date
     shall vest on the next anniversary of the Tranche B Grant Date following
     such Tranche B Performance Measurement Date; provided the Optionee is
     employed by the Company on such next anniversary of such Tranche B Grant
     Date. For purposes of this Section 7(a), the initial Tranche B Performance
     Measurement Date for any Tranche B Options granted hereunder shall be the
     Anniversary Date immediately following the Tranche B Grant Date.

   -----------------------------------------------------------------------------
   Tranche B Performance                      Tranche B Per Share
   Measurement Date                           Target Value
   -----------------------------------------------------------------------------
   First  Anniversary Date (May 28,                    $13.00
   2000)
   -----------------------------------------------------------------------------
   Second   Anniversary  Date  (May                    $16.90
   28, 2001)
   -----------------------------------------------------------------------------
   Third  Anniversary Date (May 28,                    $21.97
   2002)
   -----------------------------------------------------------------------------
   Fourth   Anniversary  Date  (May                    $28.58
   28, 2003)
   -----------------------------------------------------------------------------
   Fifth  Anniversary Date (May 28,                    $37.13
   2004)
   -----------------------------------------------------------------------------
   Sixth  Anniversary Date (May 28,                    $48.27
   2005)
   -----------------------------------------------------------------------------
   Seventh Anniversary Date                            $62.75
   (May 28, 2006)
   -----------------------------------------------------------------------------
   Eighth  Anniversary  Date                           $81.58
   (May 28, 2007)
   -----------------------------------------------------------------------------
   Ninth   Anniversary   Date                          $106.05
   (May 28, 2008)
   -----------------------------------------------------------------------------

                                       2

<PAGE>

   -----------------------------------------------------------------------------
   Tenth   Anniversary   Date                          $137.87
   (May 28, 2009)
   -----------------------------------------------------------------------------

     4. Section 8(a) of the Plan is amended in its entirety and restated to read
as follows:

          Section 8(a). Vesting Schedule. All of the Tranche C Options granted
     to an Optionee on a particular date (the "Tranche C Grant Date") shall
     become Vested Options on the date that is seven years immediately following
     the Tranche C Grant Date ("Tranche C Vesting Date") if the Optionee is
     employed by the Company on the Tranche C Vesting Date. However, if the Per
     Share Equity Value as of any of the first five Tranche C Performance
     Measurement Dates following the Tranche C Grant Date as indicated below
     (each a "Tranche C Performance Measurement Date") equals or exceeds the
     corresponding Tranche C Per Share Target Value indicated below for such
     date (the "Tranche C Per Share Target Value"), then 20% of the Tranche C
     Options issued to such Optionee on such Tranche C Grant Date shall vest on
     the next anniversary of the Tranche C Grant Date following such Tranche C
     Performance Measurement Date; provided the Optionee is employed by the
     Company on such next anniversary of such Tranche C Grant Date. For purposes
     of this Section 8(a), the initial Tranche C Performance Measurement Date
     for Tranche C Options granted hereunder shall be the Anniversary Date
     immediately following the Tranche C Grant Date.

   -----------------------------------------------------------------------------
   Tranche C Performance                       Tranche C Per Share
   Measurement Date                            Target Value
  ------------------------------------------------------------------------------
   First  Anniversary Date (May 28,                     $14.00
   2000)
   -----------------------------------------------------------------------------
   Second   Anniversary  Date  (May                     $19.60
   28, 2001)
   -----------------------------------------------------------------------------
   Third  Anniversary Date (May 28,                     $27.44
   2002)
   -----------------------------------------------------------------------------
   Fourth   Anniversary  Date  (May                     $38.42
   28, 2003)

                                       3

<PAGE>

   -----------------------------------------------------------------------------
   Fifth  Anniversary Date (May 28,                     $53.79
   2004)
   -----------------------------------------------------------------------------
   Sixth  Anniversary Date (May 28,                     $75.31
   2005)
   -----------------------------------------------------------------------------
   Seventh Anniversary Date                             $105.43
   (May 28, 2006)
   -----------------------------------------------------------------------------
   Eighth  Anniversary  Date                            $147.60
   (May 28, 2007)
   -----------------------------------------------------------------------------
   Ninth   Anniversary   Date                           $206.64
   (May 28, 2008)
   -----------------------------------------------------------------------------
   Tenth   Anniversary   Date                           $289.30
   (May 28, 2009)
   -----------------------------------------------------------------------------

     5. Except as specifically set forth herein, there are no other amendments
or modifications to the Plan.

                                       4<PAGE>

                                                                   Exhibit 10.50

                AMENDMENT NO. 2 TO THE PACER INTERNATIONAL, INC.
                             1999 STOCK OPTION PLAN

1. Amendment of Plan and Exhibits. The following amendments to the Pacer
International, Inc. 1999 Stock Option Plan, as amended by the First Amendment
thereto dated September 8, 2000 (the "First Amendment") (as so amended, the
"Plan") are adopted, effective as hereinafter provided.

     A. Section 3(a) of the Plan is hereby amended by deleting the first two
sentence thereof and inserting in their place:

     "This Plan shall be administered by a committee (the "Committee") of the
Board of Directors of the Company (the "Board"), appointed from time to time by
the Board; provided, however, that following the date on which the Common Stock
is registered under the Exchange Act, in order to permit officers and directors
of the Company to be exempt from the provisions of Section 16(b) of the Exchange
Act with respect to transactions pursuant to this Plan, each person appointed to
the Committee, at the effective date of his or her appointment to the Committee
shall, to the extent practicable, be a "Non-Employee Director" within the
meaning of Rule 16b-3 ("Rule 16b-3") promulgated by the Securities and Exchange
Commission under the Exchange Act."

     B. Section 15 of the Plan is hereby deleted in its entirety and replaced
with the following:

" 15. WITHHOLDING TAXES

     When taxable compensation is realized by an Optionee in respect of an
Option, such Optionee shall satisfy all applicable federal, state or local taxes
required by law to be withheld at such time); provided, however, that with
respect to persons subject to Section 16 of the Exchange Act, any such
withholding arrangement shall be in compliance with any applicable provisions of
Rule 16b-3 promulgated under Section 16 of the Exchange Act. The Option
Agreement shall specify the manner in which the withholding obligation shall be
satisfied with respect to the Option."

     C. Section 16(c) of the Plan is hereby deleted in its entirety and replaced
with the following:

     "(c) Amendment of Plan. This Plan may be amended by the shareholders of the
Company. This Plan may also be amended by the Board or the Committee, including,
without limitation, to the extent necessary to qualify any or all outstanding
Options granted under this Plan or Options to be granted under this Plan for
favorable federal income tax treatment (including deferral of taxation upon
exercise) as may be afforded incentive stock options under Section 422 of the
Code, to the extent necessary to ensure the qualification of this Plan under
Rule 16b-3, at such time, if any, as the Company has a class of stock registered
pursuant to

<PAGE>

Section 12 of the Exchange Act, and to the extent necessary to qualify the
shares of Common Stock issuable upon exercise of any outstanding Options
granted, or Options to be granted, under this Plan for listing or admission for
trading on any securities exchange or automated quotation system. Any amendment
approved by the Board or the Committee which is of a scope that requires
shareholder approval under applicable law or in order to ensure favorable
federal income tax treatment for any Incentive Stock Options or requires
shareholder approval in order to ensure the compliance of this Plan with Rule
16b-3 at such time, if any, as the Company has a class of capital stock
registered pursuant to Section 12 of the Exchange Act, shall be subject to
obtaining such shareholder approval. Any modification or amendment of this Plan
shall not, without the consent of an Optionee, adversely affect his or her
rights under an Option previously granted to him or her. With the consent of the
Optionee affected, the Committee may amend such Optionee's outstanding Option in
a manner which may be materially adverse to such Optionee but which is not
inconsistent with this Plan.

     D. Section 16(d) of the Plan is hereby amended by deleting each reference
to "State of Delaware" in the said paragraph and inserting in their place "State
of Tennessee."

     E. In order to give effect to the two for one stock split of the Common
Stock in the form of a stock dividend declared by the Board of Directors and
effective as of _________, 2002, in accordance with and pursuant to Section 11
of the Plan:

          (i) Section 4(b) of the Plan is hereby amended to delete the reference
to "832,000 Shares" and inserting in its place "1,664,000 Shares";

          (ii) Section 4(e) of the Plan is hereby amended to delete the
references to "277,345 Shares", "277,336 Shares" and "277,319 Shares" and
inserting in their place "554,690 Shares", "554,672 Shares" and "554,638
Shares", respectively;

          (iii) Section 4(f) of the Plan is hereby amended to delete the
references to "1,793,747 Shares" and "562,861 Shares" and inserting in their
place "3,587,494 Shares" and "1,125,722 Shares", respectively;

          (iv) Section 4(i) of the Plan is hereby amended to delete the
reference to "562,861 Shares" and inserting in its place "1,125,722 Shares";

          (v) Section 5 of the Plan is hereby amended by deleting the reference
to "$10.00" and inserting in its place "$5.00";

          (vi) Section 7(a) of the Plan as heretofore amended by the First
Amendment is hereby further amended by deleting the table in said section and
inserting in its place the following table:

<PAGE>

-----------------------------------------------------------------------
       Tranche B Performance                Tranche B Per Share
          Measurement Date                     Target Value
-----------------------------------------------------------------------
Third Anniversary Date
     (May 28, 2002)                               $10.985
-----------------------------------------------------------------------
Fourth Anniversary Date
     (May 28, 2003)                               $14.29
-----------------------------------------------------------------------
Fifth Anniversary Date
     (May 28, 2004)                               $18.565
-----------------------------------------------------------------------
Sixth Anniversary Date
     (May 28, 2005)                               $24.135
-----------------------------------------------------------------------
Seventh Anniversary Date
     (May 28, 2006)                               $31.375
-----------------------------------------------------------------------
Eighth Anniversary Date
     (May 28, 2007)                               $40.79
-----------------------------------------------------------------------
Ninth Anniversary Date
     (May 28, 2008)                               $53.025
-----------------------------------------------------------------------
Tenth Anniversary Date
     (May 20, 2009)                               $68.935
-----------------------------------------------------------------------

          (vii) Section 8(a) of the Plan as heretofore amended by the First
Amendment is hereby further amended by deleting the table in said section and
inserting in its place the following table:

-----------------------------------------------------------------------
       Tranche C Performance                Tranche C Per Share
          Measurement Date                     Target Value
-----------------------------------------------------------------------
Third Anniversary Date
     (May 28, 2002)                               $13.72
-----------------------------------------------------------------------
Fourth Anniversary Date
     (May 28, 2003)                               $19.21
-----------------------------------------------------------------------
Fifth Anniversary Date
     (May 28, 2004)                               $26.895
-----------------------------------------------------------------------

<PAGE>

-----------------------------------------------------------------------
       Tranche C Performance                Tranche C Per Share
          Measurement Date                     Target Value
-----------------------------------------------------------------------
Sixth Anniversary Date
     May 28, 2005)                                $37.655
-----------------------------------------------------------------------
Seventh Anniversary Date
     (May 28, 2006)                               $52.715
-----------------------------------------------------------------------
Eighth Anniversary Date
     (May 28, 2007)                               $73.80
-----------------------------------------------------------------------
Ninth Anniversary Date
     (May 28, 2008)                               $103.32
-----------------------------------------------------------------------
Tenth Anniversary Date
     (May 28, 2009)                               $144.65
-----------------------------------------------------------------------

          (viii) Exhibits A and B to the Plan are hereby deleted and replaced in
their entirety by Exhibits A and B hereto;

          (ix) Appendix A to the form of 1998 Rollover Options-ISO in Exhibit D
to the Plan is hereby amended by deleting the reference to "Option Price: $10"
and inserting in its place "Option Price: $5";

          (x) Appendix A to the form of 1997 Rollover Options-ISOs in Exhibit D
to the Plan is hereby deleted and replaced in its entirety by Exhibit C hereto;

          (xi) Appendix A to the form of 1997 Rollover Options-NQO in Exhibit D
to the Plan is hereby amended by deleting the references to "Common Stock:
33,483" and "Common Stock: $2.96" and inserting in their place to "Common Stock:
66,966" and "Common Stock: $1.48", respectively; and

          (xii) Appendix A to the form of New Option Grants in Exhibit D to the
Plan is hereby deleted and replaced in its entirety by Exhibit D hereto.

2. Effective Date: The effective date of Sections 1.A., 1.B., 1.C. and 1.D of
this Amendment shall be __________, 2002. The effective date of Section 1.E. of
this Amendment shall be [insert date that Articles of Amendment is filed in
Tennessee and the Stock Split is effective]

3. Terms and Conditions of Plan: Except for the above amendments, all terms and
conditions of the Plan are unamended and shall remain in full force and effect.

<PAGE>

4. Execution: This Amendment has been executed by a duly authorized officer of
the Company on the date set forth below.

                                           PACER INTERNATIONAL, INC.

                                           By:
                                               --------------------------------
                                           Title:
                                                  -----------------------------
                                           Date:
                                                 ------------------------------

<PAGE>

                                                                      EXHIBIT A

                 LIST OF INITIAL PARTICIPANTS AND INITIAL AWARDS
<TABLE>
<CAPTION>
INITIAL
PARTICIPANTS                                   INITIAL AWARDS
------------                                   --------------
                             Tranche A      Tranche B      Tranche C        Total
<S>                          <C>            <C>            <C>          <C>
Donald C. Orris               66,668         66,666         66,666        200,000
Gerry Angeli                  66,668         66,666         66,666        200.000
Gary I. Goldfein              66,668         66,666         66,666        200,000
Richard P. Hyland             66,668         66,666         66,666        200,000
Allen E. Steiner              66,668         66,666         66,666        200,000
Robert L. Cross               66,668         66,666         66,666        200,000
Robert Papworth                8,000          8,000          8,000         24,000
Dan Pendleton                  8,000          8,000          8,000         24,000
George Kirtley                10,000         10,000         10,000         30,000
Greg Steiner                  10,000         10,000         10,000         30,000
John Hein                     10,000         10,000         10,000         30,000
Russ Oldson                    6,668          6,666          6,666         20,000
Larry Kuharevicz               5,000          5,000          5,000         15,000
George Michelbach              5,000          5,000          5,000         15,000
Kent Prokop                    5,000          5,000          5,000         15,000
Mark Hyland                    5,000          5,000          5,000         15,000
Mike Amerio                    5,000          5,000          5,000         15,000
Gary Copple                    5,000          5,000          5,000         15,000
Gene Lucarz                    5,000          5,000          5,000         15,000
Debra Wilcox                   5,000          5,000          5,000         15,000
Bob Smith                      3,334          3,334          3,332         10,000
Jim Baca                       3,334          3,334          3,332         10,000
Jonathon Devens                3,334          3,334          3,332         10,000
Tom Knieps                     3,334          3,334          3,332         10,000
Patricia Hamrick               3,334          3,334          3,332         10,000
Bruce Jackson                  3,334          3,334          3,332         10,000
Bruce Hearn                    3,334          3,334          3,332         10,000
Pat McGurk                     3,334          3,334          3,332         10,000
Jerel McQuarrie                3,334          3,334          3,332         10,000
Bob Sweitzer                   3,334          3,334          3,332         10,000
Dennis Richards                3,334          3,334          3,332         10,000
Steve Hawkins                  3,334          3,334          3,332         10,000
Gary McGrath                   3,334          3,334          3,332         10,000
Jim Wade                       3,334          3,334          3,332         10,000
Jim Simon                      3,334          3,334          3,332         10,000
Mike Murrell                   3,334          3,334          3,332         10,000
Jim Silingo                    3,334          3,334          3,332         10,000
Martin Healy                   2,668          2,666          2,666          8,000
James Skelton                  2,668          2,666          2,666          8,000
TOTALS                       554,690        554,672        554,638      1,664,000
</TABLE>

<PAGE>

                                                                      EXHIBIT B

                              1997 ROLLOVER OPTIONS
<TABLE>
<CAPTION>
--------------------------------------------------------------------------------------------------------------------------
                        Rollover Options                      Rollover Options    Rollover Options     Rollover Options
      Employee          after Conversion   Exercise Price     Vested at Grant    Vesting on 3/31/00    Vesting on 3/31/01
--------------------------------------------------------------------------------------------------------------------------
<S>       <C>           <C>                <C>                <C>                <C>                   <C>
Donald    common stock  243,832 (ISOs)     243,832 (ISOs)     69,666 (NQOs)       121,916 (ISOs)       121,916 (ISOs)
Orris                                      at $0.11           at $1.48            at $0.11             at $0.11

                        69,666 (NQOs)      69,666 (NQOs)
                        69,666 (NQOs)      at $1.48
          ----------------------------------------------------------------------------------------------------------------
          preferred     11,666 (ISOs)      $9                 3,333 (NQOs)         5,833 (ISOs)        5,833 (ISOs)
          stock                                               at $9                at $9               at $9
                        3,333 (NQOs)
--------------------------------------------------------------------------------------------------------------------------
Robert    common stock  243,832 (ISOs)     243,832 (ISOs)     69,666 (NQOs)        121,916 (ISOs)      121,916 (ISOs)
Cross                                      at $0.11           at $1.48             at $0.11            at $0.11

                        69,666 (NQOs)      69,666 (NQOs)
                                           at $1.48
          ----------------------------------------------------------------------------------------------------------------
          preferred     11,666 (ISOs)      $9                 3,333 (NQOs)         5,833 (ISOs)        5,833 (ISOs)
          stock                                               at $9                at $9               at $9

                        3,333 (NQOs)
--------------------------------------------------------------------------------------------------------------------------
Gerry     common stock  243,832 (ISOs)     243,832 (ISOs)     69,666 (NQOs)        121.916 (ISOs)      121.916 (ISOs)
Angeli                                     at $0.11           at $1.48             at $0.11            at $0.11

                        69,666 (NQOs)      69,666 (NQOs)
                                           at $1.48
          ----------------------------------------------------------------------------------------------------------------
          preferred     11,666 (ISOs)      $9                 3,333 (NQOs)         5,833 (ISOs)        5,833 (ISOs)
          stock                                               at $9                at $9               at $9

                        3,333 (NQOs)
--------------------------------------------------------------------------------------------------------------------------
</TABLE>

<PAGE>

                                                          EXHIBIT B (continued)

                              1998 ROLLOVER OPTIONS
--------------------------------------------------------------------------------
Optionee            Shares of Common Stock      Exercise Price
--------------------------------------------------------------------------------
Joseph Atturio            58,728                    $4.305
--------------------------------------------------------------------------------
Lawrence Yarberry         66,000                    $5.00
--------------------------------------------------------------------------------
William Schuman           22,000                    $5.00
--------------------------------------------------------------------------------
Thomas Fitzgerald         22,000                    $5.00
--------------------------------------------------------------------------------
Brian Kane                16,500                    $5.00
--------------------------------------------------------------------------------

<PAGE>

                                                                      EXHIBIT C

                                                       Appendix A--Form of 1997
                                                          Rollover Options-ISOs

Number of Shares

         Common Stock:     243,832

         Preferred Stock   11,666

Option Price:

         Common Stock      $0.11

         Preferred Stock   $9

Vesting Schedule

                    Vests on March 31, 2000   Vests on March 31, 2001
                    ---------------------------------------------------
   Common Stock             121,916                   121,916
                    ---------------------------------------------------
 Preferred Stock          5,833 shares             5,833 shares
                    ---------------------------------------------------

<PAGE>

                                                                      EXHIBIT D

                                                        Appendix A--Form of New
                                                                  Option Grants

Number of Shares: _____
       Tranche A: _____
       Tranche B: _____
       Tranche C: _____

Option Price:              [$5] per share

Vesting Schedule

                           Tranche  B

-----------------------------------------------------------------------
       Tranche B Performance                Tranche B Per Share
          Measurement Date                     Target Value
-----------------------------------------------------------------------
Third Anniversary Date
     (May 28, 2002)                               $10.985
-----------------------------------------------------------------------
Fourth Anniversary Date
     (May 28, 2003)                               $14.29
-----------------------------------------------------------------------
Fifth Anniversary Date
     (May 28, 2004)                               $18.565
-----------------------------------------------------------------------
Sixth Anniversary Date
     (May 28, 2005)                               $24.135
-----------------------------------------------------------------------
Seventh Anniversary Date
     (May 28, 2006)                               $31.375
-----------------------------------------------------------------------
Eighth Anniversary Date
     (May 28, 2007)                               $40.79
-----------------------------------------------------------------------
Ninth Anniversary Date
     (May 28, 2008)                               $53.025
-----------------------------------------------------------------------
Tenth Anniversary Date
     (May 20, 2009)                               $68.935
-----------------------------------------------------------------------

<PAGE>

                                                           EXHIBIT D (continued)

                           Tranche C

-----------------------------------------------------------------------
       Tranche C Performance                Tranche C Per Share
          Measurement Date                     Target Value
-----------------------------------------------------------------------
Third Anniversary Date
     (May 28, 2002)                               $13.72
-----------------------------------------------------------------------
Fourth Anniversary Date
     (May 28, 2003)                               $19.21
-----------------------------------------------------------------------
Fifth Anniversary Date
     (May 28, 2004)                               $26.895
-----------------------------------------------------------------------
Sixth Anniversary Date
     May 28, 2005)                                $37.655
-----------------------------------------------------------------------
Seventh Anniversary Date
     (May 28, 2006)                               $52.715
-----------------------------------------------------------------------
Eighth Anniversary Date
     (May 28, 2007)                               $73.80
-----------------------------------------------------------------------
Ninth Anniversary Date
     (May 28, 2008)                               $103.32
-----------------------------------------------------------------------
Tenth Anniversary Date
     (May 28, 2009)                               $144.65
-----------------------------------------------------------------------

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