Warburton was commissioned in the Royal Air Force (RAF) an acting pilot officer (on probation) on 3 September 1939 and confirmed as a pilot officer on 31 October. During pilot training, Warburton struggled to achieve the minimum standard. Nevertheless, he was awarded his pilot's brevet in May 1939. Despite writing off his aircraft's undercarriage in a botched landing, he successfully completed advanced flying training and was posted to a torpedo training course at Gosport in Hampshire at the end of August 1939. He was then posted to No 22 Squadron, RAF Thorney Island, on 12 October 1939, which was operating ancient, single-engine Vickers Vildebeest biplanes. The squadron was in the process of being equipped with the advanced Bristol Beaufort torpedo bomber. Warburton's weaknesses on twin-engine aircraft were all too apparent and no attempt was made to convert him onto the Beaufort.