Protecting American Manufacturing Jobs Act of 2003 - Revises Buy America requirements applicable to Federal mass transportation assistance to define "manufactured goods" to mean each individual item specified in each line item of a procurement.
Requires the Secretary of Transportation to publish a detailed written justification in the Federal Register when issuing a waiver from Buy America provisions as to why the waiver is in the public interest. Prohibits the Secretary from granting a waiver from Buy America provisions for microcomputer equipment.
Allows any party adversely affected by an agency action related to Buy America provisions to seek administrative review under the Administrative Procedure Act.
Provides that the amendments made by this Act shall not modify the scope or terms of an existing waiver granted to microprocessors or microcomputers, including software, incorporated in certain train control or communication equipment.