"The company commander was arrested tonight by the military police and is under investigation," the army said in a statement.
It said an investigation by the military police "has raised suspicions that the version of events given by the company commander was false".
The unnamed officer had been cleared in an earlier preliminary inquiry over the shooting of 13-year-old Iman al-Hams on 5 October in the southern Gaza town of Rafah on suspicion she was carrying explosives in her school satchel.
According to a fellow soldier, the commander then fired into the girl's body several times.
The body was riddled with 20 bullets, including five in the head, the doctor who examined it told AFP.