The boy, who cannot be named for legal reasons, is due to appear at Thames Magistrates' Court today.
Shereka Marsh died at a house in Eastway, in Hackney on Saturday after being shot in the neck.
Two 16-years-olds who had been arrested in connection to the shooting have been released without charge, police said.
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A woman hit by police gunfire during a counter-terrorism operation has been arrested after being released from hospital.
Police have been granted extra time to question a man who is being held on suspicion of planning a terror attack.
The man opened fire at the house, shattering the front door and window.