Medical Neutrality Protection Act of 2013 - Requires the Secretary of State to compile and update at least annually a list of those foreign governments that the Secretary determines have engaged in violations of medical neutrality and to provide a formal notification to a foreign government included in such list. Defines a “violation of medical neutrality” to include government-sanctioned actions, and actions not authorized by a government policy but which are not independently investigated, including: (1) militarized attacks on health care facilities, health care service providers, or individuals in the course of receiving medical treatment; (2) wanton destruction of medical supplies, facilities, records, or transportation services; (3) willful obstruction of medical ethics; (4) coercion of medical personnel to commit acts in violation of their ethical responsibilities; (5) deliberate misuse of health care facilities, transportation services, uniforms, or other insignia; (6) deliberate blocking of access to health care facilities and health care professionals; or (7) arbitrary arrest or detention of health care service providers or individuals seeking medical care.

Prohibits specified presidential authorities, including the authority to transfer excess defense articles, furnish military training and education, or finance the procurement of defense articles, from being used to provide assistance to, and prohibits licenses for direct commercial sales of military equipment from being issued to, the government of a country that has engaged in a violation of medical neutrality. Makes such prohibition on assistance effective for a minimum of one fiscal year, after which the President may reinstate such assistance. Authorizes the President to temporarily waive the prohibitions in the interest of national security.

States the policy of the United States concerning the protection of medical neutrality.

Requires the Secretary to deny the issuance of a visa to any alien that is or was engaged in or has organized any act that is a violation of medical neutrality.

Directs the heads of U.S. diplomatic and consular missions to investigate all reports of violations of medical neutrality.