Zakir, an employee at the centre where the victim was enrolled, raped the girl on June 8 and threatened to kill her if she told anyone about the incident, police said.
The accused had allegedly asked the victim to stay back and committed the crime after all other students had left, they said, adding that he has been arrested.
Two days after the incident, the girl had stopped going to the centre as she could not face the accused who again threatened her, police said.
"FIR was lodged at Bisrakh police station. Zakir has been arrested," a senior police officer said.