Stop Taxing American Assistance to Afghanistan Act - Prohibits U.S. assistance for Afghanistan unless the United States and Afghanistan enter into a bilateral agreement which provides that work performed in Afghanistan by U.S. contractors is exempt from taxation by the government of Afghanistan.

Authorizes the President to waive such prohibition if in the U.S. national interest.

Makes such prohibition inapplicable to a contract: (1) under which the contractor or subcontractor is not a U.S. national, or (2) involving commercial operations of U.S. diplomatic missions in Afghanistan.