The girl's brother and a policeman were also injured in the encounter which started this morning.
Security forces this morning launched a cordon and search operation (CASO) in Kalaroos village of the district following specific intelligence inputs about the presence of militants in the area, a police official said.
He said as the forces were conducting the operation, the hiding militants fired upon them, triggering an encounter.
"Three militants have been killed in the encounter," the official said, adding the three bodies and three weapons have also been recovered from the encounter site.
He said the identity of the slain militants is yet to be ascertained.
During the gunfight, the official said, a minor girl Kaniza (12) was hit by a "stray bullet" and died on the spot while her brother Faisal was injured and has been rushed to a hospital for treatment.
He said a policeman was also injured in the initial gunfight.