He was charged at the weekend following a complaint to police by his mother.
The offence allegedly took place in the early hours of Sunday at the family home in Blackpool, Lancashire.
He is the youngest ever British male to be charged with raping his mother.
During the second hearing of his case magistrates at Preston, the boy appeared before district judge Jeff Brailsford and the court decided to allow the youth bail.
Initially District Judge Jeff Brailsford sitting at Blackpool Magistrates Court remanded the youth in custody.
However at the second hearing on Wednesday, he has been bailed on condition he lives and sleeps at an address to be decided by social services.
The teenager, whose identity cannot be disclosed for legal reasons, was released on bail ahead of a hearing at Preston Crown Court on 11 March.
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