Three students at the elite Bronx HS of Science have been busted for allegedly assaulting and threatening to rape a 15-year-old track teammate as part of a sickening hazing ritual.

Thomas Brady of The Bronx and Boubacar Diallo of Roosevelt Island, both 16, and Pier Berkmans, 17, of The Bronx, were charged with forcible touching and repeated assaults on the freshman inside the boys’ locker room from late December through Feb. 25.

All three pleaded not guilty Thursday.

A fourth, unidentified student is believed to have been involved in at least one of the attacks.

A track-team member said the alleged rape threat and assaults had crushed the victim’s spirit.

“After [one] incident, he seemed to become isolated, really upset,” the student said. “He said that, like, ‘Oh, because of that, I don’t have any friends anymore. I want to transfer out.’ ”

In a letter to parents Friday, school Principal Valerie Reidy said she was suspending all track events.

Pier’s mom, Yekaterina Berkmans, said her son is innocent — that he was a mentor, not a bully, to his accuser. Diallo’s dad referred questions to a lawyer who didn’t comment. Brady couldn’t be reached.