Humphrey transferred to No. 452 Squadron, flying Spitfires from RAF Kenley in July 1941, before becoming an instructor at No. 58 Operational Training Unit at RAF Grangemouth in August 1941. He became a Flight Commander with No. 175 Squadron flying Hurricanes from RAF Warmwell in March 1942 and was promoted to the war substantive rank of flight lieutenant on 1 May 1942 before returning to RAF Grangemouth in July 1942. Awarded the Air Force Cross on 1 January 1943, he attended the Low Attack Instructor's School at RAF Milfield in early 1943. He became a Flight Commander with No. 6 Squadron, flying Hurricanes in North Africa in July 1943, and was promoted to flight lieutenant on a permanent basis on 7 September 1943. He became an instructor at No. 5 Middle East Training School at RAF Shallufa in Egypt in January 1944 before being posted to the staff at RAF Nicosia in Cyprus in June 1944 and then to the staff at RAF Ranchi in India in November 1944. He was awarded a Bar to the Air Force Cross on 1 January 1945, and promoted to the war substantive rank of squadron leader on 20 February 1945.