Investigators say the suspect and the victim agreed to meet in the bathroom at Reservoir High School in Fulton during school hours, but she did not consent to sexual activity.
Despite her protests, police say he sexually assaulted her.
The girl reported the incident to a counselor, and police were notified.
Police charged the suspect with second-degree rape, second-degree sexual assault, and fourth-degree sex offense.
The suspect’s identity has not been released.
He was taken into custody on Wednesday, and reportedly won’t return to school while police investigate.