Police said the minor also faces aggravated assault, possession of a firearm during the commission of felony, cruelty to children 2nd degree and possession of a handgun by a person under 18.
Police said the boy turned himself in to police and is in the Youth Detention Center.
Investigators said there were able to establish probable cause and obtained warrants.
Police were called out to the Station at Richmond Hill apartment complex on southeast Atlanta's Richmond Circle around 10:15 p.m. Wednesday.
Officers found the child, Kimoni Mack, dead at the scene.
Investigators said the shooting took place inside the apartment. Police said there were no other children inside, but adults were around at the time.
Investigators initially suspected a 16-year-old was responsible for the shooting.
Police did not identify the boy facing charges.
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