By the end of 1939, Charnley's projects had been stymied by the outbreak of World War II. He joined the troops as a volunteer in the Royal Army Medical Corps on 1 May 1940 and, after a training period, he was posted to Dover as a Regimental Medical Officer. He participated in the British evacuation of Dunkirk and subsequently he was sent to 31st General Hospital at Hellingly, East Sussex. He then moved to Davyhulme Park Hospital and later to the General Hospital at Garrioch.