Firefighters were called to University of Chester Academy High School at around 6am yesterday.
12 fire crews from Cheshire Fire and Rescue were called to the school on Shipbrook Road after the fire was reported.
Two engines from Northwich and Winsford, and one from each of Middlewich, Congleton, Sandbach, Holmes Chapel, Lymm, Warrington and Altrincham attended the scene, along with the service's aerial appliance.
The blaze had broken out in two separate roofs of buildings at the school, and has created a lot of visible damage to the roof structure.
Fire crews used several mains jet and hose reels to tackle the fires, and breathing apparatus due to concerns of potential asbestos from the building fabric.
It took firefighters around three hours to bring the blaze under control, with appliances remaining on site for most of the day to dampen the fire down and ensure the site was safe.
The fire is believed to have been started deliberately and Cheshire Police are urging anyone who may have information on the incident to contact them on 101.