The incident happened at a home in the Holliswood section just after 5 p.m. Saturday.
The boy was apparently playing with the gun when it went off, striking Deaza Barkley, officials said.
EMS rushed Barkley to the hospital in critical condition, where she later died from her injury.
The 16-year-old is facing charges including manslaughter and criminal possession of a weapon.
Police are still working to uncover who owned the gun used in the shooting.
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