Palestinian Compliance Act of 2006 - Amends the Foreign Operations, Export Financing, and Related Programs Appropriations Act, 2006 to withhold financial assistance to the Palestinian Authority (PA) until presidential certification that the PA has: (1) denounced terrorism and expressed a commitment to combating terrorism; (2) committed to disarming terrorists and disarming and dismantling terrorist networks, groups, and entities; (3) committed to eliminating the incitement of terrorism and the commemoration of terrorists in Palestinian society; (4) pledged to uphold the human rights, civil liberties, and religious liberties of the Palestinian people; (5) recognized Israel's right to exist and taken appropriate steps to amend "The Covenant of the Islamic Resistance Movement" (August 18, 1988) to delete statements that are hostile to Israel and that support the use of violence; (6) renounced the use of violence as a means to resolve disputes between entities; and (7) committed to prosecuting those individuals, entities, and organizations that have committed acts of terrorism.