Appalachian Development Highway System Completion Act of 2003

Appalachian Development Highway System Completion Act of 2003 - Authorizes appropriations out of the Highway Trust Fund (other than the Mass Transit Account) for the Appalachian development highway system program for each of FY 2004 through 2009. Directs the Secretary of Transportation to apportion such funds among the States based on the latest available cost-to-complete estimate for the system, prepared by the Appalachian Regional Commission.

Authorizes a State, upon notice to the Secretary, to lend any amount of contract or obligation authority available to it pursuant to the apportionment to any other State that is eligible for such an apportionment for use for eligible activities with respect to the system.

Provides that whenever an apportionment is made, the Secretary shall deduct an amount (not to exceed two-fifths of one percent of the sums made available) determined to be appropriate to administer provisions concerning the program and to make transfers to the Commission to pay the costs of administrative activities associated with the system.

Removes the system from minimum guarantee provisions under Federal highway law.