Ending Federal Marijuana Prohibition Act of 2013

Ending Federal Marijuana Prohibition Act of 2013 - Directs the Attorney General to issue a final order that removes marijuana in any form from all schedules of controlled substances under the Controlled Substances Act.

Amends such Act to: (1) provide that schedules I, II, III, IV, and V shall consist of the drugs and other substances that are set forth in the respective schedules in part 1308 of title 21 of the Code of Federal Regulations; (2) exempt marijuana from such Act except as provided in this Act; (3) revise the definition of "felony drug offense" to exclude conduct relating to marijuana; and (4) eliminate marijuana from provisions setting forth penalties applicable to prohibited conduct under such Act.

Prohibits shipping or transporting marijuana from any place outside a jurisdiction of the United States into such a jurisdiction in which its possession, use, or sale is prohibited.

Eliminates marijuana as: (1) a controlled substance for purposes of the Controlled Substances Import and Export Act or the National Forest System Drug Control Act of 1986, (2) a dangerous drug for purposes of federal criminal code provisions authorizing interception of communications, and (3) a targeted drug for purposes of provisions of the national youth anti-drug media campaign under the Office of National Drug Control Policy Reauthorization Act of 1998.

Amends the Federal Alcohol Administration Act to set forth procedures for the issuance and revocation by the Secretary of the Treasury of permits for importing, shipping or selling in interstate or foreign commerce, purchasing for resale, producing, packaging, or warehousing marijuana. Prohibits any person from engaging in such conduct without a permit, subject to a $1,000 fine and/or a $500 payment. Sets forth criteria for ineligible applicants and disqualifying offenses.

Subjects marijuana to the provisions that apply to: (1) intoxicating liquors under the Original Packages Act, the Webb-Kenyon Act, and the Victims of Trafficking and Violence Protection Act of 2000; and (2) distilled spirits under the Federal Alcohol Administration Act.

Grants the Food and Drug Administration (FDA) the same authorities with respect to marijuana as it has for alcohol. Transfers functions of the Administrator of the Drug Enforcement Administration (DEA) relating to marijuana enforcement to the Director of the Bureau of Alcohol, Tobacco, Firearms, and Explosives (ATF). Renames: (1) ATF as the Bureau of Alcohol, Tobacco, Marijuana, Firearms and Explosives; and (2) the Alcohol and Tobacco Tax and Trade Bureau as the Alcohol, Tobacco, and Marijuana Tax and Trade Bureau.

Directs the Comptroller General to review federal laws, regulations, and policies to determine if changes are desirable in light of this Act.