According to police, S. Xavier, Principal of Tilaiya Public School, was arrested after the girl's father filed a complaint against him at the Tilaiya police station.
The principal allegedly raped the girl inside the school's washroom on November 29. When she tried to shout, he offered her a chocolate.
The girl told her mother about the assault after reaching home.
Xavier has been charged under the Protection of Children from Sexual Offences (POCSO) Act.
The principal told reporters that he has not committed "any big crime". He said he committed the crime due to tension, and termed it as "accidental"'.