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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The operation to recover the unexploded bomb near the Houses of Parliament let to disruption in central London overnight.
Southern parts of England and Wales will see sunny skies after a frosty start.
Police said the incident in Melbourne, Australia, was terror related.