National Rail Infrastructure Program Act

National Rail Infrastructure Program Act - Directs the Secretary of Transportation to establish a National Rail Infrastructure Program to provide grants for projects addressing railroad infrastructure and systems deficiencies.

Makes eligible for such grants projects to: (1) maintain and increase track and intermodal yard capacity; (2) acquire rights-of-way for future expansion; (3) separate railroad and road crossings and make other railroad and road interface improvements; (4) separate rail-to-rail crossings; (5) integrate railroad systems; and (6) construct, repair, and rehabilitate track and related supporting structures. Prohibits the use of grant funds for operating expenses, acquisition of rolling stock, payment of debt, or construction or repair of maintenance facilities, passenger facilities at stations, or other ancillary railroad business structures.

Requires at least 20 percent of project costs to be provided by State, local, and other non-Federal public sources.

Amends the Internal Revenue Code to impose an excise tax of: (1) five percent on the sale of any specified railroad equipment by the manufacturer, producer, or importer; (2) five percent of the amount paid for taxable rail transportation of any person by commuter rail, and of ten percent in any other case; and (3) one percent of the amount paid inside or outside the United States for the taxable rail transportation of property.

Establishes in the Treasury a National Rail Infrastructure Program Trust Fund, consisting of amounts equivalent to: (1) specified excise taxes received with respect to fuel used in a train, and the excise tax under this Act on railroad locomotives and rolling stock; (2) ten percent of all customs duties received after September 30, 2003; and (3) ten percent of all royalties attributable to the removal of oil or gas from Federal lands. Makes amounts in the Trust Fund available only for grants under this Act.