The Bronx district attorney's office says the teen boys, two 16-year-olds and a 17-year-old, are facing charges including forcible touching, assault and hazing.
Authorities say the teens are all on the Bronx High School of Science track team, and the alleged incidents involved another student on the team and took place between December and February.
"An allegation was brought to the attention of the school last Wednesday and three students were arrested," department spokeswoman Marge Feinberg tells MyFoxNY.com. "The matter is under investigation."
The teens pleaded not guilty at their arraignment last week and were released on their own recognizance. They are due back in court March 8.
The city Department of Education says the matter is under investigation. The school did not return a message by The Associated Press seeking comment, but Feinberg says the school's track events have been suspended pending the outcome of the investigation.
The Associated Press contributed to this report.