The nine-year-old girl was admitted to BR Ambedkar hospital in Rohini where her condition was stable, said a senior police officer.
The rape allegedly took place last Sunday. The accused had allegedly threatened the girl not to tell anyone about the incident. However, the matter came to light when her parents took her to hospital after she was taken ill.
A complaint was lodged at Narela police station.
A case was registered under the Protection of Children From Sexual Offences (POCSO) Act, he said.
The accused identified as Zakir Hussain was arrested yesterday. He taught at a madrassa in a slum of Narela, said the officer.