<PAGE>

                                                                    EXHIBIT 4.11

                                                                  Execution Copy
                                                                  --------------


                                     REGISTRATION RIGHTS
                              AGREEMENT (this "Agreement"), dated as of
                                               ---------
                              May 28, 1999, by and among COYOTE
                              ACQUISITION LLC, a Delaware limited liability
                              company ("Coyote I"), COYOTE ACQUISITION
                                        --------
                              II LLC, a Delaware limited liability company
                              ("Coyote II", and, together with Coyote I,
                                ---------
                              "Coyote"), and Pacer International, Inc., a
                               ------
                              Tennessee corporation (the "Company").
                                                          -------

                                   RECITALS

          WHEREAS, pursuant to that certain Stock Purchase Agreement, dated as
of March 15, 1999 (the "Purchase Agreement"), by and between Coyote I, and APL
                        ------------------
Limited, a Delaware corporation, Coyote I will purchase (the "Acquisition") the
                                                              -----------
number of outstanding shares of common stock, $.01 value (the "Common Stock"),
                                                               ------------
of the Company set forth in the Purchase Agreement (to the extent the right to
purchase such shares has not been assigned to one or more third parties by
Coyote I),

          WHEREAS, pursuant to that certain Assignment and Assumption Agreement,
dated as of May 28, 1999, between Coyote I and Coyote II (the "Assignment
                                                               ----------
Agreement"), Coyote I has assigned the right to purchase 5.3966 shares (563,400
---------
shares on a post-split basis) of Common Stock to Coyote II;

          WHEREAS, upon consummation of the Acquisition, Coyote will own
approximately ninety percent (93%) of the Common Stock; and

          WHEREAS, the Company desires to grant to Coyote certain registration
and other rights relating to the shares of Common Stock to be held by Coyote
(the "Coyote Shares") upon consummation of the Acquisition in accordance with
      -------------
the terms and conditions of this Agreement.

          NOW, THEREFORE, in consideration of the premises and agreements
contained herein, and for other good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, Coyote and the Company hereby
agree as follows:

     Section 1.  Definitions.  For the purpose of this Agreement:
                 -----------

          (a)  The Terms "register," "registered" and "registration" refer to a
                          --------    ----------       ------------
registration effected by filing with the Securities and Exchange Commission (the
"Commission") a registration statement or statements or similar documents in
 ----------
compliance with the Securities Act of 1933, as amended (the "Securities Act"),
                                                             --------------
and the declaration or ordering by the Commission of the effectiveness of such
registration statement.

          (b)  The term "Registrable Securities" means (i) the Coyote Shares and
                         ----------------------
(ii) any other shares of Common Stock (including shares of Common Stock
subsequently acquired by Coyote) that during the term of this Agreement become
beneficially owned by Coyote.  The term "Registrable Securities" shall also
                                         ----------------------
include any Common Stock issued as a dividend, stock split or
<PAGE>

other distribution with respect to, or in exchange for, upon reclassification or
in replacement of, Registrable Securities. In the event of any recapitalization
by the Company, whether by stock split, reverse stock split, stock dividend or
otherwise, the number of shares of Registrable Securities shall be
proportionately increased or decreased.

     Section 2.  Demand Registration.
                 -------------------

          (a)  If the Company shall receive from Coyote I or Coyote II a written
request to register shares of Registrable Securities, which request may include
an initial public offering of the Company's securities, the Company shall
prepare and file a registration statement under the Securities Act covering the
shares so requested to be registered, and shall use its best efforts to cause as
expeditiously as possible such registration statement to become effective;
provided, however, that the shares of Common Stock for which registration has
-------- --------
been requested shall constitute not less than 5% of all of the Coyote Shares (or
any lesser percentage if the reasonably anticipated aggregate price to the
public of such public offering, including, without limitation, an initial public
offering, would exceed $10 million); provided, further, that if the amount of
                                     -------- --------
Common Stock for which registration has been requested constitutes less than 5%
of all of the Coyote Shares and such amount represents all Registrable Shares,
the foregoing limitation shall not apply.  Notwithstanding anything to the
contrary contained herein, no request may be made under this Section 2 within 90
days after the effective date of a registration statement filed by the Company
covering a firm commitment underwritten public offering in which the holders of
Common Stock shall have been entitled to join pursuant to Sections 3 or 4 of
this Agreement and in which there shall have been effectively registered all
shares of Common Stock as to which registration shall have been requested.
Except as set forth above, there shall be no limit to the number of
registrations that may be requested pursuant to this Section 2; provided,
                                                                --------
however, that the Company shall be obligated to register the Common Stock
-------
pursuant to this Section 2 on no more than one occasion during any six-month
period.

          (b)  Either of Coyote I or Coyote II shall have the right to select
underwriters, if any, from time to time in connection with the sale of
Registrable Securities pursuant to this Section 2.

          (c)  The Company shall be entitled to include in any registration
statement referred to in this Section 2, for sale in accordance with the method
of disposition specified by either of Coyote I or Coyote II, shares of Common
Stock to be sold by the Company for its own account, except as and to the extent
that, in the opinion of the managing underwriter (if such method of disposition
shall be an underwritten public offering), such inclusion would adversely affect
the marketing of the Coyote Shares to be sold.  Except for registration
statements on Form S-4, S-8 or any successor forms thereto, the Company will not
file with the Commission any other registration statement under the Securities
Act with respect to its Common Stock, whether for its own account or that of
other shareholders, from the date of receipt of a notice from either of Coyote I
or Coyote II pursuant to this Section 2 until the completion of the period of
distribution of the registration contemplated thereby.

          (d)  The Company may at its option elect that any requested
registration pursuant to this Section 2 be delayed for a period not in excess of
30 days from the date of such request, such right to delay a request to be
exercised by the Company not more than once in any twelve-

                                      -2-
<PAGE>

month period (so that no such election by the Company may be made within twelve
months of a previous election by the Company under this subsection (d)).

     Section 3.     Incidental Registration.  If the Company at any time (other
                    -----------------------
than pursuant to Section 2 or Section 4 of this Agreement) proposes to register
any of its Common Stock under the Securities Act for sale to the public, whether
for its own account or for the account of other shareholders or both (except
with respect to registration statements on Forms S-4, S-8 or such other form
which is not available for registering Common Stock for sale to the public),
each such time it will give at least 20 days prior written notice to Coyote of
its intention so to do.  Upon the written request of either or both of Coyote I
or Coyote II, received by the Company within 15 days after the giving of any
such notice by the Company, to register any of their Common Stock (which request
shall state the intended method of disposition thereof), the Company will use
its best efforts to cause the Common Stock as to which registration shall have
been so requested to be included in the securities to be covered by the
registration statement proposed to be filed by the Company, all to the extent
requisite to permit the sale or other disposition by either or both of Coyote I
or Coyote II (in accordance with their written request) of such Common Stock so
registered.  Alternatively, the Company may include such Common Stock in a
separate registration statement to be filed concurrently with the registration
statement for the securities to be filed by the Company.  In the event that any
registration pursuant to this Section 3 shall be, in whole or in part, an
underwritten public offering of Common Stock for the account of the Company, the
number of Registrable Securities to be included in such underwritten public
offering may be reduced if and to the extent that the managing underwriter
advises the Company in writing that in its opinion such inclusion would
materially adversely affect the marketing of the Common Stock to be sold by the
Company therein; provided, however, that the number of such Registrable
                 -------- --------
Securities shall be reduced pro rata (based on the number of Registrable
Securities owned) with the shares of Common Stock to be registered for the
account of all persons other than the Company.  Except as set forth above, there
shall be no limit to the number of registrations that may be requested pursuant
to this Section 3.

     Section 4.  Registration on Form S-3. If at any time (a) either of Coyote I
                 ------------------------
or Coyote II request that the Company file a registration statement on Form S-3,
or any successor form thereto, for a public offering of all or any portion of
the shares of Common Stock held by them, the reasonably anticipated aggregate
price to the public of which would exceed $5 million and (b) the Company is a
registrant entitled to use Form S-3 or any successor form thereto or other short
form registration statement to register such shares of Common Stock, then the
Company shall use its best efforts to register under the Securities Act on Form
S-3 or any successor form thereto or other short form registration statement,
for public sale in accordance with the method of disposition specified in such
notice, the number of shares of Common Stock specified in such notice. Whenever
the Company is required by this Section 4 to use its best efforts to effect the
registration of Common Stock, each of the procedures and requirements of Section
2 shall apply to such registration; provided, however, that the requirements
                                    --------  -------
contained in Section 2(a) shall not apply to any registration on Form S-3 which
may be requested and obtained under this Section 4. The Company shall be
obligated to register Common Stock pursuant to this Section 4 on no more than
one occasion during any three-month period. Except as set forth above, there
shall be no limit to the number of registrations that may be requested pursuant
to this Section 4.

                                      -3-
<PAGE>

     Section 5.  Obligations of the Company.  If and whenever the Company is
                 --------------------------
required under Sections 2, 3 or 4 to effect the registration of any Registrable
Securities, the Company shall, as expeditiously as reasonably possible:

          (a)  prepare and file with the Commission a registration statement
(which, (i) in the case of an underwritten public offering pursuant to Section 2
shall be on Form S-1 or other form of general applicability satisfactory to the
managing underwriter and (ii) (A) in the case of a registration statement on
Form S-l, shall be filed within 90 days after receipt of the requisite request
from Coyote for registration and, (B) in the case of a registration statement on
any other form including Form S-2 and S-3, shall be filed within 45 days after
receipt of the requisite request from Coyote for registration) with respect to
the Common Stock and use its best efforts to cause such registration statement
to become effective, and keep such registration statement effective for up to
one hundred twenty (120) days or such longer period as the Company may agree
upon, or until the distribution has been completed, whichever occurs first;

          (b)  prepare and file with the Commission such amendments and
supplements to such registration statement and the prospectus used in connection
with such registration statement as may be necessary to keep such registration
Statement effective as provided in Section 5(a) and to comply with the
provisions of the Securities Act with respect to the disposition of all
securities covered by such registration statement;

          (c)  furnish to Coyote such numbers of copies of the registration
statement, the prospectus, including a preliminary prospectus, and of each
amendment and supplement (in each case, including all exhibits), in conformity
with the requirements of the Securities Act, and such other documents as either
of Coyote I or Coyote II may reasonably request in order to facilitate the
disposition of Registrable Securities owned by them;

          (d)  use its best efforts to register and qualify the securities
covered by such registration statement under such other securities or "blue sky"
                                                                       --------
laws of such states as shall be reasonably necessary to facilitate an orderly
distribution of the Registrable Securities; provided, however, that the Company
                                            -------- --------
shall not be required in connection therewith or as a condition thereto to
qualify to do business in any such jurisdiction in which, but for the
requirements of this Section 5, it would not otherwise be obligated to be so
qualified or to file a general consent to service of process in any such states
or jurisdictions; provided, further, that the Company will be required to
                  -------- --------
consent to service of process in actions arising out of or in connection with
the sale of any Registrable Securities;

          (e)  enter into such agreements (including an underwriting agreement,
if applicable, containing customary provisions including, without limitation,
representations and warranties and the requirement of an opinion of counsel) and
take such other actions in connection therewith in order to expedite or
facilitate a disposition of the Common Stock to be registered;

          (f)  use its best efforts to cause all such securities covered by such
registration statement to be listed or quoted (as the case may be) on any
securities exchange or automated quotation system on which the Common Stock is
then listed or quoted, and if the Common Stock is not already so listed or
quoted at such time, to use its best efforts promptly to cause all such
securities to be listed on either the New York Stock Exchange or the American
Stock Exchange

                                      -4-
<PAGE>

or to be quoted on the National Association of Securities Dealers Automated
Quotation System and to provide a transfer agent and registrar for such
securities covered by such registration statement no later than the effective
date of such registration statement;

          (g) use its best efforts to obtain a "cold comfort" letter or letters
                                                ------------
from the Company's independent public accountants in customary form and covering
matters of the type customarily covered by "cold comfort" letters;
                                            ------------

          (h) notify Coyote, at any time when a prospectus relating thereto is
required to be delivered under the Securities Act, upon occurrence of any event
as a result of which, or upon the Company becoming otherwise aware that, the
prospectus included in such registration statement, as then in effect, includes
an untrue statement of a material fact or omits to state a material fact
required to be stated therein or necessary to make the statements therein not
misleading in the light of the circumstances then existing, and, at the request
of either of Coyote I or Coyote II, prepare and furnish to Coyote a reasonable
number of copies of the amended or supplemental prospectus as may be necessary
so that, as thereafter delivered to investors of such securities under the
registration statement, such prospectus shall not include an untrue statement of
a material fact or a misstatement of a material fact required to be stated
therein or necessary to make the statements therein not misleading in light of
the circumstances then existing;

          (i) make available for inspection by representatives of either or both
of Coyote I or Coyote II, any underwriter participating in any disposition to be
effected pursuant to such registration statement and any attorney, accountant or
other agent retained by either or both of Coyote I or Coyote II or any such
underwriter all financial and other records, pertinent corporate documents and
properties and cause the Company's officers, directors and employees to supply
all information reasonably requested by either or both of Coyote I or Coyote II,
any underwriter and any attorney, accountant or other agent in connection with
such registration statement;

          (j) in the event of the issuance of any stop order suspending the
effectiveness of any registration statement or of any order suspending or
preventing the use of any prospectus or suspending the qualification of any
Registrable Securities for sale in any jurisdiction, use its best efforts
promptly to obtain its withdrawal;

          (k) otherwise use its best efforts to comply with all applicable rules
and regulations of the Commission, and make available to its security holders,
as soon as reasonably practicable, but not later than 18 months after the
effective date of the registration statement, an earnings statement covering the
period of at least twelve months, beginning with the first fiscal quarter
beginning after the effective date of the registration statement, which earnings
statement shall satisfy the provisions of Section 11 (a) of the Securities Act
and Rule 158 thereunder; and

          (l) cooperate and assist in any filings required to be made with the
National Association of Securities Dealers, Inc. (the "NASD") and in the
                                                       ----
performance of any due diligence investigation by Coyote (including any

"qualified independent underwriter" that is required to be retained in
----------------------------------
accordance with the rules and regulations of the NASD).

          Each of Coyote I and Coyote II agrees that, upon receipt of any notice
from the Company of the happening of any event described in Section 5(h), each
of Coyote I and Coyote

                                      -5-
<PAGE>

II will forthwith discontinue disposition of such securities pursuant to such
registration statement until Coyote's receipt of the copies of the supplemental
or amended prospectus contemplated by Section 5(h), and, as so directed by the
Company, each of Coyote I and Coyote II will deliver to the Company (at the
Company's expense) all copies, other than permanent file copies then in such
party's possession, of the prospectus covering such securities covered by such
registration statement current at the time of receipt of such notice. In the
event the Company shall give any such notice, the period mentioned in Section
5(a) shall be extended by the number of days during the period from the date of
the giving of such notice pursuant to Section 5(h) and through the date when
Coyote shall have received the copies of the supplemented or amended prospectus
contemplated by Section 5(h).

          In connection with each registration hereunder each of Coyote I and
Coyote II will furnish to the Company in writing such information with respect
to themselves and the proposed distribution by them as shall be reasonably
necessary and shall be requested by the Company in order to comply with federal
and applicable state securities laws.

          In connection with each registration pursuant to Sections 2, 3 or 4
covering an underwritten public offering, the Company and each of Coyote I and
Coyote II agree to enter into a written agreement with the managing underwriter
in such form and containing such provisions as are customary in the securities
business for such an arrangement between such underwriter and companies of the
Company's size and investment stature.

     Section 6.     Expenses.  All expenses incurred by the Company in complying
                    --------
with Sections 2, 3 and 4, including, without limitation, all registration and
filing fees, printing expenses, fees and disbursements of counsel and
independent public accountants for the Company, fees and expenses (including
counsel fees and expenses) incurred in connection with complying with state
securities or "blue sky" laws, fees of the NASD, transfer taxes, fees of
               --------
transfer agents and registrars, costs of insurance and reasonable fees and
disbursements of one counsel for the sellers of Common Stock, but excluding any
Selling Expenses (as defined below), are herein referred to as "Registration
                                                                ------------
Expenses." "Selling Expenses" as used herein mean all underwriting discounts and
--------    ----------------
selling commissions applicable to the sale of Common Stock.

          The Company will pay all Registration Expenses in connection with each
registration statement under Sections 2, 3 or 4.  All Selling Expenses in
connection with each registration statement under Sections 2, 3 or 4 shall be
borne by the participating sellers of Common Stock in proportion to the number
of shares sold by each, or by such participating sellers of Common Stock other
than the Company (except to the extent the Company shall be a seller of Common
Stock) as they may agree.

     Section 7.     Indemnification and Contribution.
                    --------------------------------

          (a) In the event of a registration of any Common Stock under the
Securities Act pursuant to Sections 2, 3 or 4, the Company will indemnify and
hold harmless, to the full extent permitted by law, each of Coyote I and Coyote
II and each of their respective officers, directors and affiliates and each
person controlling either of Coyote I or Coyote II, with respect to any
registration, qualification, listing or compliance effected pursuant to Sections
2, 3 and 4 of this

                                      -6-
<PAGE>

Agreement, and each underwriter, if any (including any broker or dealer which
may be deemed an underwriter), and each person who controls any underwriter
(including any such broker or dealer), against any losses, claims, damages,
liabilities and expenses, joint or several, to which they may become subject
under the Securities Act, the Securities Exchange Act of 1934, as amended (the
"Exchange Act"), or other federal and state laws or otherwise, insofar as such
 ------------
losses, claims, damages or liabilities (or actions in respect thereof) arise out
of or are based upon any untrue statement or alleged untrue statement of any
material fact contained in any registration statement under which such Common
Stock was registered under the Securities Act pursuant to Sections 2, 3, or 4,
any preliminary prospectus or final prospectus contained therein, or any
amendment or supplement thereto, or arise out of or are based upon the omission
or alleged omission to state therein a material fact required to be stated
therein or necessary to make the statements therein not misleading, and will pay
or reimburse each of Coyote I and Coyote II, each such underwriter and each such
director, officer and affiliate and controlling person for any legal or other
expenses reasonably incurred by them in connection with investigating or
defending any such loss, claim, damage, liability or action; provided, however,
                                                             --------  -------
that the Company will not be liable in any such case if and to the extent that
any such loss, claim, damage or liability arises out of or is based upon an
untrue statement or alleged untrue statement or omission or alleged omission so
made in conformity with information furnished by Coyote I, Coyote II, any such
underwriter or any such controlling person, as the case may be, in writing
specifically for use in such registration statement, prospectus, amendment or
supplement and which solely relates to Coyote I, Coyote II, any such underwriter
or any such controlling person, as the case may be.

          (b)  In the event of a registration of any Common Stock under the
Securities Act pursuant to Sections 2, 3 or 4, Coyote I and Coyote II will
indemnify and hold harmless the Company, each person, if any, who controls the
Company, each officer of the Company who signs the registration statement, each
director of the Company, each underwriter and each person who controls any
underwriter against all losses, claims, damages or liabilities, joint or
several, to which the Company or such officer, director, underwriter or
controlling person may become subject under the Securities Act, the Exchange Act
or other federal or state laws or otherwise, but only insofar as such losses,
claims, damages or liabilities (or actions in respect thereof), arise out of or
are based upon an untrue statement or alleged untrue statement or omission or
alleged omission to state therein a material fact required to be stated therein
or necessary to make the statements therein not misleading, made in reliance
upon and in conformity with information pertaining solely to Coyote I or Coyote
II, as appropriate, furnished in writing to the Company by Coyote I or Coyote
II, as appropriate, specifically for use in such registration statement under
which such Common Stock was registered under the Securities Act pursuant to
Sections 2, 3 or 4, any preliminary prospectus or final prospectus contained
therein, or any amendment or supplement thereof, and will pay or reimburse the
Company and each such officer, director, underwriter and controlling person for
any legal or other expenses reasonably incurred by them in connection with
investigating or defending any such loss, claim, damage, liability or action;
provided, however, that (i) the liability of either of Coyote I or Coyote II
-------- --------
hereunder shall be limited to the proportion of any such loss, claim, damage,
liability or expense which is equal to the proportion that the public offering
price of the shares of Common Stock sold by such entity under such registration
statement bears to the total public offering price of all securities sold
thereunder, but not in any event to exceed the net proceeds received by such
entity from the sale of Common Stock covered by such registration statements and
(ii) neither of Coyote I or Coyote

                                      -7-
<PAGE>

II shall be liable for amounts paid in settlement of any such loss, claim,
damage, liability or action if such settlement is effected without the consent
of Coyote, such consent not to be unreasonably withheld or delayed.

          (c)  Promptly after receipt by an indemnified party hereunder of
written notice of any claim or the commencement of any action or proceeding,
such indemnified party shall, if a claim in respect thereof is to be made
against the indemnifying party hereunder, notify the indemnifying party in
writing thereof, but the omission so to notify the indemnifying party shall not
relieve it from any liability which it may have to such indemnified party other
than under this Section 7 and shall only relieve it from any liability which it
may have to such indemnified party under this Section 7 if and to the extent the
indemnifying party is materially prejudiced by such omission.  In case any such
action shall be brought against any indemnified party and the indemnified party
shall notify the indemnifying party of the commencement thereof, the
indemnifying party shall be entitled to participate in and, to the extent it
shall wish, to assume and undertake the defense thereof with counsel reasonably
satisfactory to such indemnified party, and, after notice from the indemnifying
party to such indemnified party of its election so to assume and undertake the
defense thereof, the indemnifying party shall not be liable to such indemnified
party under this Section 7 for any legal or other professional expenses
subsequently incurred by such indemnified party in connection with the defense
thereof other than reasonable costs of investigation and of liaison with counsel
so selected; provided, however, that if the defendants in any such action
             -------- --------
include both the indemnified party and the indemnifying party, and the
indemnified party shall have reasonably concluded that there may be reasonable
defenses available to it which are different from or additional to those
available to the indemnifying party or if the interests of the indemnified party
reasonably may be deemed to conflict with the interests of the indemnifying
party, the indemnified party shall have the right to select a separate counsel
and to assume such legal defenses and otherwise to participate in the defense of
such action, with the reasonable fees and expenses of such separate counsel and
other expenses related to such participation to be reimbursed by the
indemnifying party as incurred.  No indemnifying party, in the defense of any
such claim or litigation against an indemnified party, shall consent to entry of
any judgment or enter into any settlement which does not include as an
unconditional term thereof the giving by the claimant or plaintiff to such
indemnified party of a release from all liability in respect of such claim or
litigation, unless such indemnified party shall otherwise consent in writing.
An indemnifying party who is not entitled to, or elects not to, assume the
defense of a claim shall not be obligated to pay the fees and expenses of more
than one counsel for all parties indemnified by such indemnifying party with
respect to such claim, unless any indemnified party reasonably concludes that
there may be legal defenses available to such indemnified party with respect to
such claim which are different from or additional to those available to any
other of such indemnified parties or that a conflict of interest may exist
between such indemnified party and any other of such indemnified parties with
respect to such claim, in which event the indemnifying party shall be obligated
to pay the reasonable fees and expenses of such additional counsel or counsels.

          (d)  If the indemnification provided for in this Section 7 is for any
reason held by a court of competent jurisdiction to be unavailable to an
indemnified party in respect of any claims referred to therein, then the
indemnifying party, in lieu of indemnifying such indemnified party thereunder,
shall contribute to the amount paid or payable by such indemnified party as a
result of such claims (i) in such proportion as is appropriate to reflect the
relative benefits received by

                                      -8-
<PAGE>

the indemnifying party and the indemnified party, or (ii) if the allocation
provided by clause (i) above is not permitted by applicable law, in such
proportion as is appropriate to reflect not only the relative benefits referred
to in clause (i) above but also the relative fault of the indemnifying party and
the indemnified party in connection with the action or inaction which resulted
in such claims, as well as any other relevant equitable considerations. In
connection with any registration of the Company's securities, the relative
benefits received by the indemnifying party and the indemnified party shall be
deemed to be in the same respective proportions that the net proceeds from the
offering (before deducting expenses) received by the indemnifying party and the
indemnified party, in each case as set forth in the table on the cover page of
the applicable prospectus, bear to the aggregate public offering price of the
securities so offered. The relative fault of the indemnifying party and the
indemnified party shall be determined by reference to, among other things,
whether the untrue or alleged untrue statement of a material fact or the
omission or alleged omission to state a material fact relates to information
supplied by the indemnifying party or the indemnified party and the parties'
relative intent, knowledge, access to information and opportunity to correct or
prevent such statement or omission.

     Section 8.     Rule 144 Reporting and Other Requirements.
                    -----------------------------------------

          (a)  With a view to making available the benefits of certain rules and
regulations of the Commission which may at any time permit the sale of the
Common Stock to the public without registration, at all times after any
registration statement covering a public offering of securities of the Company
under the Securities Act shall have become effective, the Company agrees to:

               (i)   make and keep public information available, as those terms
     are understood and defined in Rule 144, or any successor rule thereto,
     under the Securities Act (such rule or its successor, "Rule 144");
                                                            --------

               (ii)  use it best efforts to file with the Commission in a timely
     manner all reports and other documents required of the Company under the
     Securities Act and the Exchange Act; and

               (iii) furnish to Coyote I or Coyote II forthwith upon request a
     written statement by the Company as to its compliance with the reporting
     requirements of such Rule 144 and of the Securities Act and the Exchange
     Act, a copy of the most recent annual or quarterly report of the Company,
     and such other reports and documents so filed by the Company as Coyote I or
     Coyote II may reasonably request in availing itself of any rule or
     regulation of the Commission allowing Coyote I or Coyote II to sell any
     Common Stock without registration.

          (b)  Whenever either of Coyote I or Coyote II undertakes to resell or
otherwise distribute Registrable Securities pursuant to Rule 144A, and in the
event the Company shall not be subject to either Section 13 or 15(d) of the
Exchange Act, the Company shall, upon request from either of Coyote I or Coyote
II, furnish to Coyote and to prospective purchasers identified by either of
Coyote I or Coyote II, a disclosure document containing the following
information:

                                      -9-
<PAGE>

                 (i)    a brief statement of the nature of the Company's
     business and the products and/or services offered by it;

                 (ii)   the Company's audited financial statements (including
     the balance sheet and profit and loss and retained earnings statements) for
     the most recent two fiscal years; and

                 (iii)  such other information as required or necessary to
     comply with the Securities Act.

     Section 9.  Entire Agreement.  This Agreement constitutes the entire
                 ----------------
agreement of the parties and supersedes all prior written or oral agreements,
contemporaneous oral agreements, understandings and negotiations between the
parties with respect to the subject matter hereof.

     Section 10. Governing Law.  This Agreement shall be construed in
                 -------------
accordance with and governed by the laws of the State of New York, without
regard to the conflicts of law rules thereof.

     Section 11. Consent to Jurisdiction.  The parties hereto hereby consent
                 -----------------------
and agree that they shall commence any action with respect to any claims or
disputes between the parties hereto pertaining to this Agreement or to any
matter arising out of or related to this Agreement in the United States District
Court for the Southern District of New York, so long as the action falls within
the subject matter jurisdiction of such court.  In the event any such action
shall be determined by the court to be outside its subject matter jurisdiction,
then the parties agree to commence any such action in the Supreme Court of New
York County, New York and to take such action as may be necessary to effect
assignment of such action to the Commercial Part of that court.  The parties
hereto expressly submit and consent in advance to such jurisdiction in any
action or suit commenced in any such court, and hereby waive any objection which
it may have based upon lack of personal jurisdiction, improper venue or forum
non conveniens and hereby consent to the granting of such legal or equitable
relief as is deemed appropriate by such court. Each party hereto irrevocably
consents to the service of process by registered or certified mail, postage
prepaid, to it at its address given in accordance herewith.

     Section 12. Amendments and Waivers.  This Agreement may not be modified,
                 ----------------------
amended or waived except by written document specifically identifying this
Agreement and signed by the parties.

     Section 13. Headings.  The headings included in this Agreement are for
                 --------
convenience of the parties only and shall not affect the construction or
interpretation of this Agreement.

     Section 14. Notices.  All notices hereunder shall be in writing and shall
                 -------
shall be given to the respective parties by U.S. mail, personal delivery or
facsimile transmission to their respective addresses as follows:

                                      -10-
<PAGE>

          If to the Company:

          Pacer International, Inc.
          3746 Mt. Diablo Blvd.
          Suite 110
          Lafayette, CA 94549
          Attn:      Donald C. Orris
          Facsimile: (303) 623-5115

          If to either of Coyote I or Coyote II:

          Coyote Acquisition Corp.
          c/o Apollo Management, L.P.
          1301 Avenue of the Americas
          New York, New York 10019
          Attn:      Joshua J. Harris
          Facsimile: (212) 515-3263

          with a copy to:

          Morton A. Pierce, Esq.
          Douglas L. Getter, Esq.
          Dewey Ballantine LLP
          1301 Avenue of the Americas
          New York, New York 10019
          Facsimile:  (212) 259-6333

          All such notices shall be deemed effective upon receipt.

     Section 15.  Successors and Assigns.  This Agreement shall be binding upon
                  ----------------------
the parties hereto and their respective successors and permitted assigns.

     Section 16.  Remedies, Waivers.  No failure or delay on the part of any
                  -----------------
party in the exercise of any power, right or privilege hereunder shall operate
as a waiver thereof, nor shall any single or partial exercise of any such power,
right or privilege preclude other or further exercise thereof or of any other
right, power or privilege.  Any waiver or consent shall be effective only in the
specific instance and for the specific purpose for which it was given.  The
parties to this Agreement acknowledge and agree that the breach of any of the
terms of this Agreement will cause irreparable injury for which an adequate
remedy at law is not available. Accordingly, it is agreed that either party
shall be entitled to an injunction, restraining order or other equitable relief
to prevent breaches of this Agreement and to enforce specifically the terms and
provisions hereof in any court of competent jurisdiction in the United States or
any state thereof without the requirement of posting any bond.  All fights and
remedies existing under this Agreement are cumulative to, and not exclusive of,
any fights or remedies available under this Agreement or otherwise.

     Section 17.  Severability.  In the event that any provision of this
                  ------------
Agreement or the application of any provision hereof is declared to be illegal,
invalid or otherwise unenforceable

                                      -11-
<PAGE>

by a court of contempt jurisdiction, such provision shall be reformed, if
possible, to the extent necessary to render it legal, valid and enforceable, or
otherwise deleted, and the remainder of this Agreement shall not be affected
except to the extent necessary to reform or delete such illegal, invalid or
unenforceable provision.

     Section 18.  Termination.  The provisions of this Agreement shall terminate
                  -----------
and be of no further effect upon (a) as to all parties, the mutual consent of
the parties and (b) as to either of Coyote I or Coyote II, such entity ceasing
to own or have rights to acquire Registrable Securities.

     Section 19.  Further Assurances.  Each party shall cooperate and take such
                  ------------------
action as may be reasonably requested by the other party in order to carry out
the provisions and purposes of this Agreement and the transactions contemplated
hereby.

     Section 20.  Counterparts.  This Agreement may be executed in counterparts,
                  ------------
each of which shall be deemed an original, but which together shall constitute
one and the same instrument.

                                      -12-
<PAGE>

          IN WITNESS WHEREOF, the parties hereto have executed and delivered
this Agreement as of the day and the year first above written.

                              PACER INTERNATIONAL, INC.


                              By: /s/ Donald C. Orris
                                 ---------------------------------------------
                                 Donald C. Orris
                                 President and Chief Executive Officer

                              COYOTE ACQUISITION LLC


                              By: /s/ Marc Becker
                                 ---------------------------------------------
                                 Marc Becker
                                 Vice President

                              COYOTE ACQUISITION II LLC


                              By: /s/ Marc Becker
                                 ---------------------------------------------
                                 Marc Becker
                                 Vice President