The accused, identified as Ranjith, had allegedly misbehaved with the class VI student at the school two days ago, police said.
"The girl informed her parents about the matter who lodged a complaint yesterday," L B Nagar police station inspector P Kasi Reddy told PTI.
A case under section 354 (assault or criminal force to woman with intent to outrage her modesty) of IPC was registered against Ranjith who has been taken into custody, Reddy said.