The accused, both 18-year-old boys, are pursuing 'religious education' in the same campus run by a minority educational and charity organisation.
They have been charged under IPC 376 (rape) and relevant provisions of Protection of Children from Sexual Offences Act, police said.
The alleged molestation took place on October 30 and a case was registered earlier this week based on the complaint from the child's parents.
A few days after the incident, the child started showing signs of pain and uneasiness and told her parents of the torture she underwent. She complained that two senior boys lured her to the kitchen on the campus and sexually abused her.
She was taken to a hospital for medical examination and it was confirmed that she suffered sexual torture.
The delay in the arrest had sparked strong public protests in the area with political parties and social activists accusing police of trying to shield the real culprits.
A bus cleaner was taken into custody yesterday in connection with the case, but was let off later after local people marched to the police station alleging that police was trying to take the investigation into wrong leads under pressure from the school management.
The institution has classes from LKG to plus-two and also a wing on the campus for religious education.