The alleged crime had taken place on the school premises, police said, adding that it came to light on November 21, when the girl was taken to a hospital and was found to be 13-weeks pregnant.
"The victim and the accused, who studied in the same school, knew each other. They had a physical relationship inside the ladies toilet of their school in August," a police officer said.
Thereafter, the accused started calling the victim regularly and forced her to keep sexual relations with him by threatening to reveal their status to their school friends, police said.
Shocked parents of the victim and the doctors contacted Juhu Police following which the girl's statement was recorded and based on her complaint, an offence against the accused was registered.
The offence has been registered at Juhu police station under Sections 354 (assault or criminal force to woman with intent to outrage her modesty), 376 (rape) and 506 r/w 4, 8 (criminal intimidation) of the IPC as well as under the Protection of Children from Sexual Offences (POCSO) Act.