Humphrey joined the Royal Air Force College Cranwell in January 1939 and was granted a permanent commission as a pilot officer on 30 April 1940. Following flying training he was posted as a pilot to No. 266 Squadron at RAF Wittering in September 1940 and found himself flying Spitfires in the Battle of Britain. In March 1941 he was involved in an incident when his engine failed and his Spitfire crashed in flames, but he survived. He was promoted to the war substantive rank of flying officer on 1 May 1941. On a single night in May 1941, he shot down one bomber and two other enemy aircraft near the Dutch coast: he was awarded the Distinguished Flying Cross for this on 30 May 1941.