An Australian Army soldier has been charged with raping a 16-year-old girl at the Gallipoli Barracks at Enoggera in Brisbane.

Police alleged the girl was smuggled past security in the boot of a car on January 14.

The ABC understands another soldier dropped her home the next day.

The 24-year-old man was charged on Wednesday with one count of rape. He was later released on watch house bail.

He is due to appear in the Brisbane Magistrates Court on February 26.

The Department of Defence said it was assisting Queensland police with their inquiries.

"Defence takes all allegations of unacceptable behaviour very seriously and investigates these matters thoroughly," it said in a statement.

"As the matter is under investigation by the Queensland Police Service it would be inappropriate for Defence to comment."