Emergency services have been called to the Island learning centre on Albany Road in Newport just before 4pm this afternoon.
The call came after a pupil had climbed onto the roof and smashed windows.
The pupil remains on the roof and is refusing to come down.
Police officers from Hampshire Constablary and the Isle of Wight fire service have been called.
A cordon has been erected outside by the school and the road has been closed to traffic in both directions.
Fire crews are using a short extension ladder in an attempt to try and engage with the distressed pupil.
UPDATE 4.15pm A member of the fire service has climbed on to the roof and is currently engaging with the youngster.
The Island Learning Centre provides specialised alternative provision for the most vulnerable students on the Isle of Wight. The school relocated to Albany Road after the previous establishment in Lake was burnt to the ground.
UPDATE 5.05pm The student has been safely brought down from the roof after a conversation with the incident commander. The incident is said to be being dealt with as an internal matter by the school. The student was not injured.