It is the first time that the appeals process has been used since it was created by Congress in late 2006 to handle cases involving Guantanamo detainees.
Omar Ahmed Khadr, a Canadian citizen, is one of two detainees whose military trials fell apart because they were not identified as "unlawful" enemy combatants.
The other is Yemeni detainee Salim Ahmed Hamdan, a former driver for Osama bin Laden.
Prosecutors filed an appeal in Khadr's case with the Court of Military Commission Review on July 4, said Navy Lt. Cmdr. Chito Peppler, a Pentagon spokesman.
Peppler said both sides will be given an opportunity to file written briefs.
Khadr and Hamdan are the only ones currently in the roughly 375-prisoner population at Guantanamo who have been charged with crimes under a reconstituted military trial system. The judge who threw out the charges against Hamdan has not yet ruled on prosecutors' motion to reconsider. Hamdan is accused of conspiracy and providing support for terrorism.
One other detainee charged under the new system, Australian David Hicks, pleaded guilty in March to providing material support to al-Qaida and is serving a nine-month sentence in Australia.
Khadr has been in custody since he was 15. He is charged with tossing a grenade that killed one U.S. soldier and injured another in Afghanistan in 2002.
He is the son of an alleged Al Qaeda financier, and his family has received little sympathy in Canada, where they've been called the "First Family of Terrorism."
Canadian Foreign Minister Peter MacKay has said the government will wait until the appeals process has been exhausted before asking U.S. authorities to release Khadr to Canada.