Staff Sergeant Shane Werst was charged on Thursday with killing Nasir Ismail after he was taken into custody during an operation in the Iraqi city of Balad on 3 January.
Spokesman Lieutenant-Colonel Jonathan Withington would not say how Ismail died, but charges were filed within days after another soldier came forward to report the alleged crime.
Werst, who has served 13 years in the US army, was also charged on Wednesday with obstruction of justice for allegedly ordering other soldiers to lie about the incident, the army said.
If convicted, he could be sentenced to life in prison without possibility of parole. No trial date has been set.
At least four other soldiers from the same barracks face charges for alleged crimes in Iraq.
Sergeant 1st Class Tracy Perkins and 1st Lieutenant Jack Saville are accused of pushing two Iraqis off a bridge into the Tigris River in January as punishment for violating curfew. One of the men drowned.
Perkins, 33, is scheduled for trial next month on charges of manslaughter, conspiracy, assault and lying to investigators. Saville, 24, will be tried in January.
In another incident, Captain Shawn Martin and Staff Sergeant Ceolia Turner are accused of "unauthorised treatment of Iraqi individuals" for a reported incident near al-Rutba between May and July.
Both face charges of assault and aggravated assault.