Sgt. Bowe Bergdahl will also be charged with misbehavior before the enemy, said the official, who was not authorized to discuss the announcement publicly on the record and spoke on condition of anonymity.
The US military plans an announcement later.
Bergdahl walked away from his post in Afghanistan and was captured, then released from Taliban capture in a prisoner exchange.
Gen. Mark Milley, head of US Army Forces Command, has been reviewing the massive case files and had a broad range of legal options, including various degrees of desertion charges.