The victim's father approached police last night and lodged an FIR in this connection, a police official said.
The matter came to light 15 days ago, when the victim narrated his ordeal to parents, the official said.
The accused Naman Chauhan, coach of a cricket academy at Morta village, Delhi-Meerut road, has been booked under section 377 IPC, said Station House Officer of Sihani Gate police station Ranvir Singh said.
The boy has been sent for medical examination and the case is under investigation, he said. "We are waiting for the medical report. The coach will be nabbed soon, if found guilty," the SHO added.