Promoted to flying officer in November 1939, Aitken remained on instructional duties into mid-1940, interspersed with periods of duty aboard a series of aircraft carriers, beginning with HMS "Courageous" and then HMS "Furious". He later served on HMS "Ark Royal" and on one voyage in February 1940, he was swept into the sea when the ship was taking evasive action during a bombing attack mounted by the Luftwaffe. The only man lost overboard in the incident, he was picked up by a following destroyer. During the campaign in Norway, Aitken flew a Hawker Hurricane off "Ark Royal" to Trondheim.