Sergeant Bowe Bergdahl was charged with misbehavior before the enemy, which carries a maximum sentence of up to life in prison. He was also charged with desertion, which carries a maximum of five years.
Bergdahl could also face a dishonorable discharge, reduction in rank and forfeiture of all his pay if convicted.
The case now goes to an Article 32 hearing to be held at Fort Sam Houston, Texas. That proceeding is similar to an investigating jury. From there, it could be referred to a court-martial and go to trial.
The charges are the latest development in a long and bitter debate over Bergdahl's case. They also underscore the military and political ramifications of his decision on June 30, 2009, to leave his post after expressing misgivings about the US military's role, as well as his own, in the Afghanistan war.
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After leaving his post, Bergdahl was captured by the Taliban and held by members of the Haqqani network, an insurgent group tied to the Taliban that operates both in Pakistan and Afghanistan.
Last May 31, Bergdahl was handed over to US special forces in Afghanistan as part of an exchange for five Taliban commanders who were imprisoned at Guantanamo Bay, Cuba.
The exchange set off a debate over whether the US should have released the five Taliban members. Little is known about what the five have been doing in Qatar, where they are being monitored by the government. Some lawmakers have predicted that the five would return to the battlefield.
Senator Lindsey Graham has said that he received information that one of the five has been in touch with members of the Haqqani network.