Police said the headmaster of the school at Soorangudi had sexually harassed the fifth standard student for some days in his room after class hours.
On September 12, he again did so following which she started crying. On hearing her sobs, some students came to the room, but were sent away by the headmaster.
Police said the girl informed her parents only yesterday, after which they filed a complaint and the headmaster was arrested.
Various sections of IPC like 342 (punishment for wrongful confinement and 506 (punishment for criminal intimidation) and 3 and 4 of Protection of Children from Sexual Offences Act 2012 were slapped against him, they said.
The girl was sent to Tirunelveli medical college hospital this morning for tests, police said.