Army vehicles were on their way to the village of Howora in Kulgam, when clashes began. Faced with stone-pelting, the Army opened fire.
The boy who was injured has been taken to the district hospital in Anantnag.
The police registered a FIR, and investigations have begun.
Jammu and Kashmir Chief Minister Mehbooba Mufti said the Army hadn't filed a counter FIR, the Indo-Asian News Service reported Saturday.