Elworthy served in the Second World War, initially in a training role with No. 108 Squadron and then, having been promoted to the temporary rank of squadron leader on 1 March 1940 (made permanent in April 1942) he became Chief Flying Instructor with No. 13 Officer Training Unit in April 1940. He was appointed a flight commander with No. 82 Squadron flying Blenheims from RAF Watton in August 1940 and then Officer Commanding No. 82 Squadron in December 1940. He was awarded the Air Force Cross in the 1941 New Year Honours on 1 January 1941 and the Distinguished Flying Cross on 7 March 1941. In March 1941, despite heavy and accurate anti-aircraft fire, he scored a direct hit on an enemy tanker, setting it on fire: he was awarded the Distinguished Service Order for this on 22 April 1941.