The police have arrested a 29-year-old man, an auto driver following a complaint by the girl's parents.
According to the complaint, the Class 9 student was allegedly sexually assaulted on August 20.
He had taken his niece in his auto to drop her back home from school but had diverted and committed the crime.
The girl has been sent for medical examination.
Dr Vijayakumar, SP of Vellore told NDTV, "There is primary facie evidence and we are investigating."