The onset of war in September 1939 had the immediate effect of totally disrupting the life of the school. Walthamstow was an evacuable area under the Government's regulations, though at first Chingford was not. The school was convened early on Monday 28 August, when war was judged imminent. There followed a week spent waiting, which was occupied largely in games, the holidays officially continuing.  

Evacuation took place on 2 September, the school being accommodated in a special L.M.S. train from Black Horse Road Station to Ampthill in Bedfordshire. Ampthill is an ancient market town, but a very small one. The boys were billeted both in the town itself and in the surrounding villages of Marston Moretaine, Maulden, and Lidlington. Groups of boys, ranging from 45 to 100, were billeted in each place, and four or five masters accompanied each contingent. Attached to the party were the younger brothers (and sisters) of the Monoux boys. At Lidlington, the villagers were expecting a party of primary schoolgirls, and at Maulden (to quote from a contemporary account) "one master found himself doomed to share a solitary single bed with four others".  

Lessons, from 16 September, took place in various church halls in Ampthill, in the Wesleyan Chapel and the Union Chapel. Lessons were somewhat attenuated in scope at first, since there were no textbooks, ink or blackboards. Evening, weekend, and in some cases, afternoon, activities had to be organised, and these took the form of walks, filling sandbags, helping local farmers, A.R.P., first-aid, and games, including one euphemistically known as "progressive table tennis".