A student at Como Park Senior High School was arrested on Wednesday after bringing a loaded handgun to school.
The 16-year-old student had the gun in his waistband, before it was confiscated and he was arrested.
St. Paul Public Schools put out an announcement on its Facebook page confirming the incident, saying the school resource officer immediately responded.
"The weapon was confiscated without incident," it adds. "No threats were made to students or staff. Saint Paul Police are investigating the incident. Police have said there are no active threats at the school."
St. Paul police told the Pioneer Press that a staff member made the school resource officer aware of the gun, and got backup via an officer from another school before going to the student's classroom.
The boy was taken from class, with police finding the 9mm handgun in his waistband.
He's been arrested on suspicion of possession of a firearm by a minor and possession of a firearm in a school.
Tensions remain high in schools across the country following the shooting in Parkland, Florida last month left 17 dead and prompted widespread calls from teenagers for stricter gun control measures.
Multiple schools in Minnesota were the subject of copycat threats of violence in the wake of the shooting, but these seem to have subsided in recent weeks.