A 16-year-old and a 17-year-old were busted with a firearm in a Bronx high school Tuesday afternoon, police said.

The loaded weapon was found inside one student’s bookbag at Bathgate High School at 1594 Bathgate Ave. around 1 p.m., cops said.

The two minors were in custody.

“Dangerous items of any kind are not tolerated in our schools,” schools spokesman Nathaniel Styer said.

“Our outstanding school staff and School Safety Agents immediately and safely recovered this item, ensuring that all students and staff are safe. All protocols were followed, and we are working closely with NYPD regarding follow-up actions.”

The 17-year-old has had several run-ins with the law dating back to June 24, when he was arrested for the alleged rape of a 13-year old at a Crotona playground in the Bronx, law enforcement sources said.

On Jan. 24, the teen was arrested by Port Authority police in the Oculus at the World Trade Center for allegedly making some kind of threat, sources said. He was charged with assaulting an officer, resisting arrest and creating a hazardous condition, according to the sources.

He was arrested again March 2 on Park Avenue and East 187th Street and found with a loaded .32 caliber pistol, the sources said. He was reportedly charged with criminal possession of a weapon.

“We are not going to win the battle when you let a young criminal like this out on the street,” a Bronx cop told The Post. “The mayor has to understand this the reality.”