Firefighters arrived at the school, located at 39600 Logan Drive, around 7:15 p.m. after community members reported seeing smoke.
Crews found flames coming from the locker room area. The one-alarm fire was controlled within 30 minutes, and was confined to an interior wall, according to the fire department.
Principal Brian Weems arrived shortly after the fire was extinguished.
"It was not as bad as I thought it would be," Weems said. "It just affected the wall between the boys' and girls' locker rooms."
Fire investigators estimated the damage at about $100,000, and Weems said evaluators from the insurance company would be doing their own assessment this afternoon.
Classes, which begin Wednesday, will not be affected, Weems said.
"It may cause problems depending on if there is asbestos or smoke residue that we don't want the children to breathe," he said. "It will be sealed off completely if that's the case."
Tests will be completed by the end of the week to determine if there are any health hazards, he said.
Weems said the locker rooms are only used for physical education classes.
"Classes will still take place. They just won't change (clothes)," he said of students.
Fremont fire Capt. Gerry Fogel said investigators believe the fire was set intentionally, but it is not clear whether the perpetrators are affiliated with the school.
Weems said that since he became principal last year, there have not been any acts of vandalism. He said he is grateful to neighbors for reporting the blaze.
"The community called the fire station before the alarm even went off," he said. "Their quick response minimized the damage."
