Harper joined the Royal Air Force (RAF) in 1937, and was commissioned as an acting pilot officer on 5 September. He was promoted to flying officer on 12 February 1940, and attached to No. 17 Squadron. On 18 May 1940 he shared in the destruction of a Messerschmitt Bf 110 heavy fighter, and a week later he destroyed a Ju 87 "Stuka" dive bomber. He was appointed B Flight commander, with the rank of acting flight lieutenant, on 26 May. He destroyed another Bf 110 over Dunkirk three days later, during the evacuation of Allied forces, and continued as flight commander until 8 June 1940, reverting to the rank of flying officer. He was again promoted to acting flight lieutenant on 4 July, when he was given command of A Flight.