In 1899 almost the entire school was destroyed by fire.
An enthusiastic pupil was boiling some snail shells in the Natural History room, but was forced away when the bell for reading time began, and the snails were left on the boil all night...resulting in an enormous fire that destroyed the gymnasium, schoolrooms, workshop, laboratories, observatory, and masters' room. When the fire brigade informed the headmaster that his school was burning down he promptly resigned; and the school had to be transferred to a temporary location on Oliver's Mount in Scarborough.

Arthur Rowntree was then appointed head and rebuilding work began.The school was reopened in 1902, and at the same time it acquired properties along Bootham and Portland Street, and the new school took shape. The swimming baths were built in 1914; and Joseph Rowntree donated Penn house in 1920. Rawcliffe Lane Playing Fields were purchased in 1920 in memory of the old boys killed in the Great War. In the post-war period a large extension was required to accommodate the new 11-13 age range of pupils. A model of the proposed building was constructed and exhibited on a fund-raising mission around the UK in a van, which for some reason was impounded when it reached Ireland. The van travelled 2000 miles in total and raised £50,000. The building at the heart of school life today is the award-winning School Hall, designed by the architect Trevor Dannatt.