Aragonez on Thursday was in the Bell County Jail on bond topping $2 million. No attorney was listed for the soldier.
The Killeen Daily Herald reports an October assault involved an 11-year-old girl. A 9-year-old girl was attacked in December.
Police arrested Aragonez during a Jan. 12 traffic stop. Investigators say DNA evidence has linked him to the attacks.
A spokesperson for Fort Hood did not immediately return a message Thursday from The Associated Press.