Protecting Taxpayers in Transportation Asset Transfers Act

Protecting Taxpayers in Transportation Asset Transfers Act - Directs the Secretary of Transportation (DOT) to establish a program for: (1) the attachment of federal liens to public transportation assets (federal-aid highways, highway or mass transit projects, air navigation facilities, or federally-assisted train or multimodal stations); and (2) release of such liens in connection with concession agreements between state or local governments and private individuals or entities.

Limits the meaning of public transportation asset to a transportation facility constructed, maintained, or upgraded before, on, or after enactment of this Act using federal funds: (1) whose fair market value is more than $500 million, and which has received any federal funding; (2) whose fair market value is less than $500 million, and which has received $25 million or more in federal funding; or (3) in which a significant national public interest (such as interstate commerce, homeland security, public health, or the environment) is at stake.

Prohibits any asset transaction (entry into a concession agreement for, or contract for the sale or lease of, a public transportation asset) for an asset attached with a federal lien unless: (1) the lien is released, and (2) the state or local government and the private individual or entity seeking the asset transaction enter into agreements with the Secretary.

Defines "concession agreement" as one entered into by a private individual or entity and a state or local government with jurisdiction over a public transportation asset to convey to the private individual or entity the right to manage, operate, and maintain the asset for a specific period of time in exchange for the authorization to impose and collect a toll or other user fee from a person for each use of the asset during that period.

Prohibits the release of a federal lien on a public transportation asset unless: (1) the state or local government or other public sponsor seeking the asset transaction pays the Secretary an amount determined according to a specified formula, and (2) the Secretary certifies that the required concession agreements have been signed and their terms incorporated into the asset transaction terms.

Permits a private individual or entity to enter into an asset transaction covering National Railroad Passenger Corporation (AMTRAK) facilities and equipment provided certain conditions are met.