The incident came to light on Wednesday, when the Vile Parle-based victim informed her mother about the episode. They went to Juhu police station and lodged a case.
The accused Ramesh Rajput was arrested yesterday and has been remanded in police custody till February 1.
According to police officials, after finishing her school on Tuesday, the minor boarded the bus that regularly dropped her home. After all the other kids had alighted, Rajput allegedly took the girl to the backseat and violated her inside the moving vehicle.
The accused then threatened the girl of dire consequences if she informed anyone. However, the victim, who was in pain, confided in her mother the next day about what had happened to her.
Rajput has been charged under sections 376 (rape), 354 (molestation), 509 (insulting modesty) of IPC and The Protection of Children from Sexual Offences Act 2012. Police said the victim has undergone a medical test, results of which are awaited. They are interrogating Rajput and the bus driver has been made a witness in the case.