Parvesh (21) allegedly kidnapped the minor girl on Saturday morning when she was returning home with her younger sister, Superintendent of Police Syed Waseem said.
The accused was arrested following a complaint by the girl's family, Waseem said.
Parvesh yesterday confessed to the crime, the SP said, adding, the girl's body was recovered with her throat slit from the toilet of a primary school.
Postmortem report has confirmed rape, he said.