Firefighters were called to the bronze age site at 3.30am on Sunday morning, but were unable to save the wooden structure.
The classroom was used for clay modelling.
Security is now being reviewed at the site.
A spokesperson for City College Peterborough Foundation, which runs the site said: “We can confirm that a building at Flag Fen used for clay modelling was destroyed by a fire in the early hours of Sunday morning. The building contained no artefacts or collections, just classroom tables and chairs.
“Following the incident, we have worked to restore electricity to buildings at the site and will be reviewing security measures there.”
A spokesman for Cambridgeshire Fire and Rescue Service said: “Crews arrived to find a wooden educational classroom totally destroyed by fire.
“Firefighters used a sumo pump and jet to extinguish the fire and dampen down the area.
“The cause of the fire was deliberate. Anyone with information should contact police by visiting cambs.police.uk to submit an online report or call Crimestoppers on 0800 555111.