The 20-year-old Samad Ali has been arrested from his home here for allegdly killing the girl, a class VII student, after committing rape, the police said.
On Friday, the girl's parents had filed a missing diary in the Raiganj police station.
A top police officer said Ali had confessed to his crime during questioning.
The arrested would be produced in the court of the North Dinajpur Chief Judicial Magistrate tomorrow.