National Park System Visitor Facilities Trust Fund Act - Establishes in the Treasury the National Park System Visitor Facilities Fund, which shall consist, with an exception, of an amount equal to all National Park System concession fees (including building user fees and rental payments collected under this Act on facilities constructed with monies from the Fund), paid to or due and owing to the United States, after September 30, 1989, to provide visitor accommodations and services in units of the National Park System.

Requires the Secretary of the Interior to include in the budget estimate for the National Park Service, a list of projects proposed to be funded with monies from the Fund during the fiscal year following the fiscal year of the enactment of this Act. Provides that monies from the Fund may be expended only when appropriated. Makes such appropriated Funds available to the Secretary for expenditure without fiscal year limitation for specified purposes.

Authorizes the Secretary to require a concessioner to complete projects with monies appropriated from the Fund.

Sets forth requirements for all projects proposed to be completed with monies from the Fund.

Directs the Secretary to collect fair rental value for the use of any visitor facility improved in whole or in part with monies from the Fund, except that if payment of such rental value is inconsistent with certain Federal law, the Secretary may waive or reduce such rental.

Prohibits: (1) any possessory interest from being recognized in any portion of any facility improved with monies from the Fund; and (2) monies from the Fund from being used to acquire any such interest in any facility.