Officials from the police special victims unit said Wednesday that the assault happened at about 4:30 a.m. Wednesday in the Feltonville section of the city.
Police said the girl told police that she awoke to find a naked man inside her room.
She said he got clothes from elsewhere in the house, carried her outside to a nearby alley and assaulted her, then told her to go home.
Capt. John Darby said officers found physical evidence of a sexual assault and the girl was treated for injuries consistent with an assault.
Darby said the girl described the assailant as wearing a green mask over part of his face.