Though the Governors continued to keep as much control as possible during the war, there was little they could do to prevent a considerable amount of decay setting in. As a school, Scorton ceased to function, and as a depot if war it became derelict.

In the early part of the war there was a struggle for survival which was lost. In 1940, the staff was reduced to help to overcome financial difficulties. At this time, there were only thirty three boys left (fifteen boarders and eighteen day boys). The workshop was taken over by the Army Search Light Corps, and in the summer of 1941, the school was closed and the premises were requisitioned for military purposes and taken aver by the R.A.F.

Two years later, the school pavilion had fallen into such a state of ruin that the sale of the wood remains realised only £1. In the same year on December 20th, there was a fire in the Headmasters house which almost resulted in the whole building being gutted.

In 1944, the government de requisitioned the school, and while the ground floor was used as a store, the upper part of the building was let to the Home Guard. There was a further suggestion that the building should become a YMCA hostel, but nothing ever became of this.

In the field at the back of the school was a hostel for agricultural workers, suitably camouflaged to avoid discovery from the air. Later this was to be of great use to the school