The girl, a student of class VI, in a police complaint, alleged that the principal, Dinesh Kumar, had yesterday asked her to stay back after the school got over on pretext of some work and then raped her.
The principal, who owns the private school where the incident happened, threatened the girl of dire consequences if she narrated the incident to anyone, police said.
On reaching home, the girl told her parents about the incident who then lodged a complaint with police in this regard.
Further investigations into the case are on, they said.