Ghulam Shahid was taken into custody as he was aware of the crime committed on the 10-year-old girl at the madrasa premises, the police said.
A probe into the incident was transferred to the Crime Branch yesterday.
The girl was rescued on April 22 from the madrasa by a Delhi Police team. The police were informed on April 21 by the girl's father that his daughter had gone missing after she went to market.
Subsequently, the girl was rescued from the madrasa and the juvenile apprehended, the police said.
The victim had recorded her statement in front of a magistrate on April 23. She said the juvenile had taken her to the madrasa to meet his friends.
The girl's parents had also been demanding the arrest of the cleric as they alleged that the man was aware about the crime.