Agricultural Job Opportunity Benefits and Security Act of 1998 - Directs the Secretary of Labor to establish a database system of U.S. agricultural worker registries to provide temporary and seasonal agricultural job opportunity and referral information.

Bases registry coverage on job opportunities in a State or group of contiguous States with a common pool of workers. Sets forth individual registrant requirements, including validation of employment status.

(Sec. 4) Requires an employer (including employer associations) prior to hiring a temporary agricultural worker to apply to the Secretary for a U.S. worker referral from the appropriate registry. Sets forth provisions regarding: (1) employer application and labor- related assurance requirements; and (2) registry search and worker referral by the Secretary, including alien worker visa issuances in cases of insufficient registered workers.

(Sec. 7) Sets forth employer requirements regarding: (1) wages; (2) housing, including an allowance in lieu of housing; and (3) transportation reimbursement, including establishment of a pilot program to provide certain registered workers with vouchers to purchase employment location transportation.

(Sec. 8) Directs the Secretary to establish an enforcement process with respect to employer application violations, including: (1) written notice of finding and opportunity for administrative appeal; (2) payment of back wages; (3) civil monetary penalties; and (4) temporary and permanent program disqualification.

(Sec. 9) Amends the Immigration and Nationality Act to replace the existing H-2A temporary agricultural worker admissions program with an alternative admissions program. Sets forth provisions regarding: (1) admissibility criteria; (2) length of stay; (3) abandonment of employment; (4) issuance of identification and employment documents; and (5) extension of stay for aliens in the United States. Establishes a trust fund in the Treasury to administer such program, and to provide monetary incentives for alien workers to return to their country of origin upon a finding by the Attorney General that such financial inducements are necessary to assure departures.

Prohibits admission of H-2A alien family members.

(Sec. 10) Includes certain H-2A workers who have complied with applicable visa conditions in the employment-based immigration preference allocation.

(Sec. 11) Amends the Head Start Act to make certain seasonal agricultural worker families eligible for the migrant and seasonal (as added by this section) Head Start program. Increases the set-aside for specified Head Start programs.

(Sec. 13) States that additional funds for the registry program, if necessary, shall come from amounts available to Federal and State entities under the Wagner-Peyser Act.