Up to 15 firefighters were called to the blaze at Walmer Science College in Salisbury Road, Deal, at 0015 BST.
The school caretaker raised the alarm after spotting the fire had been started underneath a temporary classroom.
Crews used specialist equipment to stop the fire from spreading and it was brought under control by 0415 BST.
Fire investigators and Kent Police are visiting the school to establish the cause.
A spokeswoman for Kent Fire and Rescue Service said: "We asked police to attend the scene as crews believed the fire was started deliberately."
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