The girl, who was staying with her paternal aunt after her mother passed away, was lured by her classmate on August 29 to a nearby field where he raped her, they said.
After returning home, she complained of stomach-ache to her aunt who took her to a nearby clinic where the whole matter came to light.
A police complaint was registered only after villagers staged a protest outside the Masuri police station.
Superintendent of Police (Rural) Jagdish Sharma said identity of the accused boy will soon be established with the help of the girl.