Authorities were initially told the girl's five-year-old brother had inadvertently pulled the trigger on Saturday afternoon in the city's Kensington area.
Maurice Phillips, 30, fled the house after the shooting, reports the Philadelphia Inquirer. It is unclear if he was the girl's father or step-dad.
Authorities said Phillips turned himself in to a police station on Saturday night and confessed to the shooting.
Sgt Eric Gripp said: "After investigation, (he) admitted to accidentally shooting the victim, and stated that the sibling had nothing to do with it."
Charges are pending, he added.
Police recovered a semi-automatic pistol from the scene.
Neighbours described the girl as outgoing and playful.
They said she and her siblings rarely left their home because their mother feared violence in the neighbourhood.