<PAGE>

                                                                           10.42

                        KEWAUNEE SCIENTIFIC CORPORATION
                           PENSION EQUALIZATION PLAN
                            (Effective May 1, 1999)
<PAGE>

                        KEWAUNEE SCIENTIFIC CORPORATION
                           PENSION EQUALIZATION PLAN
                            (Effective May 1, 1999)

<TABLE>
<S>                                                          <C>
Article I............................................         1
     Establishment and Purpose.......................         1
        1.1      The Plan............................         1
        1.2      Purpose.............................         1
        1.3      Plan Year...........................         1

Article II...........................................         1
     Administration and Participation................         1
        2.1      Administration......................         1
        2.2      Participation.......................         2

Article III..........................................         3
     Amount and Payment of Benefits..................         3
        3.1      Amount of Benefit...................         3
        3.2      Time and Form of Payment............         3
        3.3      Vesting.............................         4
        3.4      Death Benefits......................         4

Article IV...........................................         4
     Payment.........................................         4
        4.1      Source of Payment...................         4
        4.2      Withholding Taxes...................         4
        4.3      Disabled or Missing Participants....         5
        4.4      Claims..............................         5

Article V............................................         6
     General Provisions..............................         6
        5.1      Interests Not Transferable..........         6
        5.2      Plan Not an Employment Contract.....         7
        5.3      Effect on Other Benefit Plans.......         7
        5.4      Funding.............................         7
        5.5      Litigation..........................         8
        5.6      Cooperation.........................         8
        5.7      Severability........................         9
        5.8      Applicable Law......................         9

Article VII..........................................         9
     Amendment and Termination.......................         9

Exhibit A............................................        11
     List of Initial Participants....................        11
</TABLE>
<PAGE>

                        KEWAUNEE SCIENTIFIC CORPORATION
                           PENSION EQUALIZATION PLAN
                            (Effective May 1, 1999)

                                  Article I.
                                  ---------
                           Establishment and Purpose
                           -------------------------

     1.1  The Plan.  The KEWAUNEE SCIENTIFIC CORPORATION PENSION EQUALIZATION
          --------
PLAN (the "Plan") was established by Kewaunee Scientific Corporation (the
"Company"), effective May 1, 1999.

     1.2  Purpose.  The Plan is intended to be an unfunded "top-hat" plan
          -------
maintained for the purpose of providing a select group of management or highly
compensated employees with the full amount of retirement income that they or
their beneficiaries would be entitled to receive under the Re-Established
Retirement Plan for Salaried Employees of Kewaunee Scientific Corporation (the
"Retirement Plan") but for the limits imposed by the Internal Revenue Code on
the amount of compensation taken into account under the Retirement Plan.  The
purpose of the Plan is to advance the interests of the Company by providing such
retirement income so as to attract and retain such employees and make their
compensation competitive with other opportunities.

     1.3  Plan Year.  The Plan is maintained by the Company on the basis of a
          ---------
"Plan Year" which commences on May 1 of each calendar year and ends on April 30
of the following calendar year.

                                  Article II.
                                  ----------
                       Administration and Participation.
                       --------------------------------

     2.1  Administration.  Full power and authority to construe, interpret and
          --------------
administer the Plan shall be vested in a committee (the "Committee") composed of
the Compensation Committee of the Board of Directors of the Company.  The
Committee shall make each
<PAGE>

determination provided for under the Plan and promulgate such rules and
regulations as may be required for the implementation or management of the Plan.
The Committee may delegate all or any portion of its authority to such persons
as it may determine, and may revoke or revise any such delegation at any time.
Unless and until otherwise determined by the Committee, the authority of the
Committee to establish rules, regulations and procedures that are administrative
or ministerial in nature shall be exercised by the Company's Vice President of
Human Resources (or such other officer or employee of the Company as may occupy
a comparable position). The determinations of the Committee, or of any person to
whom the Committee's authority has been delegated, shall be final and binding on
all persons (except for the right of appeal set forth in Section 4.4).

     2.2  Participation.  Participation in the Plan shall be limited to a
          -------------
select group of management or highly compensated employees of the Company.  The
initial Participants in the Plan are listed on Exhibit A hereto.  Additional
management or highly compensated employees shall become Participants only upon
being recommended for participation by the President of the Company and approved
by the Committee.  The mere fact that any employee receives compensation in
excess of the amount that may be taken into account under the Retirement Plan
shall not in itself entitle the employee to participate in the Plan.  Nothing
contained in the Plan shall confer upon any Participant any right to be
continued in the employ of the Company or interfere in any way with the right of
the Company to terminate a Participant's employment at any time.

                                      -2-
<PAGE>

                                 Article III.
                                 -----------
                        Amount and Payment of Benefits.
                        ------------------------------

     3.1  Amount of Benefit.  The benefit payable to each Participant, or to
          -----------------
any beneficiary of a Participant, pursuant to this Plan shall be equal to the
excess, if any, of (i) the benefit that would have been payable to such
Participant or beneficiary under the Retirement Plan if the Participant's
compensation taken into account under the Retirement Plan were not limited under
Section 401(a)(17) of the Internal Revenue Code (or any successor to such
provision, as determined by the Committee), over (ii) the benefit actually paid
to such Participant or beneficiary under the Retirement Plan.  In no event shall
the sum of the benefit paid under the Retirement Plan and the benefit paid under
this Plan exceed the benefit that would have been paid under the Retirement Plan
in the absence of Section 401(a)(17) of the Code.

     3.2  Time and Form of Payment. Benefits payable under this Plan to any
          ------------------------
Participant or beneficiary shall be paid at the same time and in the same form
as the benefits paid to the Participant or beneficiary under the Retirement
Plan, taking into account any elections made by the Participant under the
Retirement Plan.  Each Participant or beneficiary shall receive at the time each
benefit payment is made pursuant to the Retirement Plan a supplemental payment
under this Plan equal to the difference, if any, described in Section 3.1.
Notwithstanding the foregoing, (i) the Committee may in its sole discretion at
any time accelerate the payment of any benefits due to any Participant or
beneficiary under this Plan, in which event the remaining amount owed to such
Participant or beneficiary shall be reduced by the actuarial equivalent of the
accelerated payment, and (ii) if the actuarial present value of the benefits due
to any Participant or beneficiary at the time benefits are due to commence does
not exceed $20,000, the amount of such present value shall be paid to such
Participant or beneficiary in a single lump sum, which

                                      -3-
<PAGE>

shall fully discharge all obligations to such Participant or beneficiary under
the Plan. For purposes of the preceding sentence, actuarial equivalent shall be
determined on the basis of the factors used for comparable computations under
the Retirement Plan.

     3.3  Vesting.  A Participant's benefits under this Plan shall be vested
          -------
to the same extent as his benefit under the Retirement Plan and shall be
forfeited only if and to the extent his Retirement Plan benefit is forfeited.

     3.4  Death Benefits.  A Participant's beneficiary under this Plan shall
          --------------
be the person entitled to receive any survivorship benefits payable with respect
to such Participant under the Retirement Plan, and such beneficiary shall be
entitled to the supplemental payments with respect to such survivorship benefits
described in Section 3.2 above.  Except for such payments, no survivorship or
other benefits shall be payable to any person by reason of the death of the
Participant.

                                  Article IV.
                                  ----------
                                   Payment.
                                   -------

     4.1  Source of Payment.  All benefits payable under this Plan shall be
          -----------------
paid either directly by the Company, or by a distribution from the Irrevocable
Grantor Trust described in Section 5.4.  The establishment and funding of the
Irrevocable Grantor Trust shall not relieve the Company of its obligations under
this Plan, but all amounts actually paid to a Participant or beneficiary from
the Irrevocable Grantor Trust shall reduce the obligation of the Company to the
extent of such payment.

     4.2  Withholding Taxes.  The Company may withhold from a Participant's
          -----------------
compensation or any payment under this Plan any taxes required to be withheld
with respect to benefits under this Plan.

                                      -4-
<PAGE>

     4.3  Disabled or Missing Participants.  If any person entitled to the
          --------------------------------
payment of benefits under the Plan is under a legal disability, or in the
Company's opinion, is incapacitated in any way so as to be unable to manage his
financial affairs, the Committee may direct the payment of such distribution to
such person's legal representative or to a relative or friend of such person for
such person's benefit.  If the Company is unable to locate any Participant or
beneficiary, and the Participant or beneficiary fails to contact the Company
after being notified of his right to receive a benefit by a letter sent to his
last address on file with the Company, then the Committee may, in its
discretion, either cause such benefit to be paid to another member of the
Participant's family or treat such benefit as forfeited.  Any payments or
forfeiture made in accordance with this Section 4.3 shall discharge fully all
obligations for such benefits under the Plan.

     4.4  Claims.  A Participant or beneficiary, or an authorized
          ------
representative acting on his behalf (hereinafter called the "claimant"), may
notify the Committee of a claim for benefits under the Plan.  Such notice may be
made in writing on a form specified by the Committee and shall set forth the
basis of such claim and shall authorize the Committee to conduct such
examinations as may be necessary to determine the validity of the claim and to
take such steps as may be necessary to facilitate the payment of any benefits to
which the claimant may be entitled under the terms of the Plan.

     Claims shall initially be processed by the person to whom the Committee's
authority over administrative matters has been delegated pursuant to Section
2.1, or such person as he may designate.  Whenever a claim for benefits by the
claimant has been denied, a written notice of denial shall be given to the
claimant, prepared in a manner calculated to be understood by him without legal
assistance and setting forth the specific reasons for the denial and explaining
the

                                      -5-
<PAGE>

procedure for an appeal and review of the decision by the Committee.  Such
notice shall be furnished not later than 90 days after the claim has been filed
(which 90 day period may be extended for up to an additional 90 days if special
circumstances require and notice of the extension is furnished to the claimant
prior to the end of the first 90 day period).

     A claimant whose claim is denied, or his authorized representative, may
request a review upon written application to the Committee within 60 days after
receiving notice of the denial.  In connection with such application, the
claimant or his authorized representative may review pertinent documents and may
submit issues and comments in writing.  If such an application is made, the
Committee shall make a full and fair review of the denial of the claim and shall
make a decision not later than its first meeting that is held at least 30 days
after receipt of the application, unless special circumstances (such as the need
to hold a hearing) require an extension of time, in which case a decision shall
be made as soon as possible but not later than the second such meeting.  If a
request for review is received at a time when the Committee does not hold
regularly scheduled meetings at least once a quarter, the decision shall be made
not later than 60 days after the request is received, which may be extended to
up to 120 days if special circumstances require.  The decision on review shall
be in writing and shall include specific reasons for the decision and specific
references to the pertinent provisions of the Plan on which the decision is
based.

                                  Article V.
                                  ---------
                              General Provisions.
                              ------------------

     5.1  Interests Not Transferable.  The interests of the Participants and
          --------------------------
their beneficiaries under the Plan are not subject to the claims of their
creditors and may not be voluntarily or involuntarily transferred, assigned,
alienated, or encumbered.  Notwithstanding the foregoing, the

                                      -6-
<PAGE>

Company may offset against any benefits payable to or on behalf of any
Participant any amount owed to it or to any of its affiliates by such
Participant, and may withhold payment of any such benefit until the amount owed
by such Participant has been determined.

     5.2  Plan Not an Employment Contract.  This Plan is not an employment
          -------------------------------
contract.  It does not give to any person the right to be continued in
employment, and all employees remain subject to change of salary, transfer,
change of job, discipline, layoff, discharge, or any other change of employment
status.

     5.3  Effect on Other Benefit Plans.  Amounts credited or paid under this
          -----------------------------
Plan, and the amount of any pay reduced pursuant to section 3.1, shall not be
considered to be compensation for the purposes of any qualified plan maintained
by the Company.  The treatment of such amounts under other employee benefit
plans shall be determined pursuant to the provisions of such plans.

     5.4  Funding.  The Company shall make payment of its contributions under
          -------
the Plan to the Company's Irrevocable Grantor Trust (which has been established
in connection with this Plan), either in cash or by the delivery to the trustee
thereunder of insurance contracts, in such amounts as the Company shall
reasonably decide are necessary to provide for all benefits payable under the
Plan.  The establishment and funding of the Irrevocable Grantor Trust shall not
relieve the Company of its obligations under this Plan, but any amount actually
paid by the Irrevocable Grantor Trust to a Participant or beneficiary shall be
credited against the amount owed by the Company to such Participant or
beneficiary under the Plan.  No employee shall have any right, title, or
interest whatever in or to any insurance contracts, investment reserves,
accounts, funds or grantor trusts that the Company may purchase, establish, or
accumulate to aid in providing the benefits under this Plan.  Neither an
employee nor a beneficiary of an employee shall acquire any

                                      -7-
<PAGE>

interest greater than that of an unsecured creditor of the Company. Any assets
of the Company or of any trust or other fund of the Company from which Plan
benefits may be paid shall remain in all respects assets of the Company until
payments of such benefits are actually made. Nothing contained in this Plan, and
no action taken pursuant to its provisions, shall create a trust or fiduciary
relationship of any kind between the Company and an employee or any other
person.

     5.5  Litigation.  In any action or proceeding regarding the Plan,
          ----------
Participants or their beneficiaries or any other persons having or claiming to
have an interest in this Plan shall not be necessary parties and shall not be
entitled to any notice or process.  Any final judgment which is not appealed or
appealable and may be entered in any such action or proceeding shall be binding
and conclusive on the parties hereto and all persons having or claiming to have
any interest in this Plan.  To the extent permitted by law, if a legal action is
begun against the Company, its officers or employees, the Committee, or the
Trustee by or on behalf of any person and such action results adversely to such
person or if a legal action arises because of conflicting claims to a
Participant's or other person's benefits, the costs to such person of defending
the action will be charged to the amounts, if any, which were involved in the
action or were payable to the Participant or other person concerned.  To the
extent permitted by applicable law, acceptance of participation in this Plan
shall constitute a release of the Company, its officers, employees and agents,
and the Committee from any and all liability and obligation not involving
willful misconduct or gross neglect.

     5.6  Cooperation.  As a condition of participation under the Plan, each
          -----------
Participant agrees to cooperate in providing all information required to carry
out the Plan, including taking such physical examination and providing such
medical history as may be required to obtain insurance with respect to such
Participant.

                                      -8-
<PAGE>

     5.7  Severability.  In the event any provision of the Plan shall be held
          ------------
invalid or illegal for any reason, such illegality or invalidity shall not
affect the remaining parts of the Plan, but the Plan shall be construed and
enforced as if the illegal or invalid provision had never been inserted, and the
Company shall have the privilege and opportunity to correct and remedy such
questions of illegality or invalidity by amendment as provided in the Plan.

     5.8  Applicable Law.  This Plan shall be governed and construed in
          --------------
accordance with the laws of the State of North Carolina.

                                 Article VII.
                                 -----------
                          Amendment and Termination.
                          -------------------------

     The Company reserves the right to amend or terminate the Plan at any time
by resolution of the Board of Directors or by action by any person or persons
authorized by resolution of the Board, provided such amendment or termination
shall not operate to reduce the amount of benefits accrued by any Participant as
of the date of the amendment or termination.  Upon termination of the Plan, the
Board may, but shall not be required to, provide for the payment of the
actuarial equivalent of the vested benefit of some or all of the Participants in
a single lump sum payment.  The fact that one or more Participants is found to
be ineligible to participate in the Plan as a result of rules or regulations
promulgated under ERISA or by the Department of Labor shall not in itself cause
a termination of the Plan.

                                      -9-
<PAGE>

     IN WITNESS WHEREOF, the Company has caused this instrument to be executed
by its duly authorized officers on this 1st day of May, 1999, effective as of
May 1, 1999.
                                   KEWAUNEE SCIENTIFIC CORPORATION


                                   By: /s/ James J. Rossi
                                       ----------------------------------
                                   Its: Vice President of Human Resources


ATTEST:

By  /s/ D. M. Parker
    --------------------------

Its Vice President - Finance

                                      -10-
<PAGE>

                                  Exhibit A.
                                  ---------
                         List of Initial Participants.
                         ----------------------------

1.   Ron Gewin

2.   Eli Manchester, Jr.

3.   Mike Parker

4.   Kurt Rindoks

5.   Bill Shumaker

                                      -11-