School District spokesman Fernando Gallard tells Action News that the female student was allegedly attacked on Friday morning.
The incident is now being handled by the Philadelphia Police Special Victims Unit.
Both students are in the ninth grade.
According to the SVU, the two students were chatting at the top of the stairwell when, at one point, the boy went to the basement followed by the girl.
Then, police said, the boy overpowered the girl and raped her.
The girl told police she screamed for help but no one heard.
The victim went on to her first period class, police said, and apparently broke down in the middle of class. It's at that point she reported the incident to her teacher who, in turn, reported it to authorities.
The area where it happened is monitored by video cameras. The police won't confirm the video, but say they do have a solid case.
"The investigation proceeded immediately, it was aggressive to the point our investigators felt probably cause was met by day's end on Friday," said Capt. John Darby of the SVU.
The juvenile turned himself in on Tuesday and is charged with five felonies including rape and four misdemeanors. He has a hearing on Wednesday. At that point it will be determined if he's released to his family on bail, or held indefinitely for trial.
The female victim is recovering at home with her mother and the school district is providing any necessary services, Gallard said.