The incident took place on the intervening night of Wednesday and Thursday, police said.
The accused trio, identified as Rehan (22), Sonu (23) and Salim (24), were arrested yesterday.
"The 13-year-old girl, after she had complained to police, was taken to a government hospital where a medical test confirmed rape," police said, adding that a case was thereafter registered and the arrests effected.
The girl had left her Harsh Vihar home on Tuesday over some issue and her family had also lodged a report over that. She first wandered around GTB hospital and, on the intervening night of Wednesday and Thursday, reached the Bhopura border in east Delhi.
