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The alleged sex attack relates to an incident in a park off College Way, Hayes, west London, in October.
Scotland Yard said the pair would appear before magistrates in Uxbridge today.
The schoolgirl was said to have been playing with the boys when the alleged attack happened during half-term school holidays.
She went with the boys to College Park in Hayes to play on the climbing frame and swings close to Hayes Community Campus, which is part of Uxbridge College.
The children were not being supervised by any adults, detectives said at the time.
The young girl, who cannot be named for legal reasons, said she was taken to bushes at the edge of the park where she was sexually assaulted in broad daylight.
The two boys are alleged to have taken turns raping her.
Afterwards, the young girl ran home to tell her parents. Horrified, they alerted police and two boys were arrested hours later.
A Met police spokesman said the charges were made following advice from the Crown Prosecution Service (CPS).
The alleged attack was investigated by officers from the Met's specialist Sapphire Unit.
The recently re-organised unit is part of the Specialist Crime Directorate.
It is run by detectives specially trained in child sex offences who have recently interviewed the young girl.
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