The incident occurred on Thursday when the girl had accompanied her mother to fields for harvesting, Khanpur SHO SS Bhati said.
On finding the girl alone, the 16-year-old accused, a student of class VII, raped her, he said.
On the complaint of victim's family, a case was registered in the matter today, Bhati added.
A search is on to nab the absconding accused, Bhati said.
The girl has been sent for medical examination, police said, adding, the matter is being investigated.