The girl gave birth to the boy last month in the bathroom of her home in Rotherham, South Yorkshire, after complaining of stomach pains.
A 23-year-old man was arrested earlier this month and released on bail after questioning.
South Yorkshire Police said yesterday the man had been re-arrested and charged with the rape of an 11-year-old girl after DNA tests. She was in her first year at secondary school when the child was conceived. He has been bailed to appear before Rotherham magistrates on 27 September.
The girl has been released from hospital and is being looked after by relatives. She has said she wants to look aftaer her son.
Legally a child under 13 can not consent to sex, so is automatically deemed to be a victim of statutory rape.