Egypt Assistance Reform Act of 2013

Applies such restrictions to Fiji, Guinea-Bissau, Madagascar, and Sudan upon enactment of this Act.

Prohibits the U.S. government from licensing or otherwise allowing the sale, lease, or transfer of defense articles or defense services to Egypt until the Secretary certifies to Congress that providing such assistance is in U.S. national security interests and the government of Egypt: (1) continues to implement the Peace Treaty between the State of Israel and the Arab Republic of Egypt; (2) is taking appropriate measures to counter terrorism; (3) is allowing U.S. Armed Forces to transit Egyptian territory; (4) is supporting a transition to an inclusive civilian government; (5) is protecting the political and economic freedoms of all residents of Egypt, including addressing violence against women and religious minorities; and (6) continues to abide by its nuclear non-proliferation commitments.

Exempts from such restrictions defense articles and defense services for supporting counterterrorism, border and maritime security, or special operations.

Directs the Secretary to submit to Congress a comprehensive strategy for modernizing and improving U.S. security cooperation with, and assistance for, Egypt which shall seek to: (1) enhance Egypt's ability to defeat al Qaeda and other terrorist organizations operating in Egypt, and to counter terrorist radicalization; (2) improve Egypt's capacity to prevent human trafficking and the illicit movement of terrorists, criminals, weapons, and other dangerous material across Egypt's borders or administrative boundaries, especially through the Gaza Strip; (3) enhance Egypt's operational and intelligence capabilities; and (E) increase accountability to civilian authority.

Prohibits bilateral economic assistance from being made available to the government of Egypt until the Secretary certifies to Congress that: (1) providing such assistance is in the U.S. national security interest; and (2) the government of Egypt continues to implement the Peace Treaty between the State of Israel and the Arab Republic of Egypt, and is taking certain political, economic, and social measures.

Excludes from such prohibition humanitarian assistance or assistance to promote democratic elections or public participation in democratic processes.

Directs the Secretary to provide to Congress a comprehensive foreign assistance strategy for Egypt that addresses how U.S. foreign assistance can most effectively advance the objective of a secure, democratic, civilian-led Egypt that is a U.S. partner and advances regional peace.

Terminates the limitations under this title on September 30, 2016, if the Secretary certifies to Congress that Egypt: (1) continues to implement the Peace Treaty between the State of Israel and the Arab Republic of Egypt; (2) is taking appropriate measures to counter terrorism, including measures to counter smuggling into the Gaza Strip; (3) is allowing U.S. Armed Forces to transit Egyptian territory; and (4) is supporting a transition to an inclusive civilian government.

Amends the Consolidated Appropriations Act, 2012 to repeal the prohibition against the use of funds under that Act for assistance to any country whose elected head of government is deposed by military coup or decree.