In 1939, when the Second World War started, Refshauge joined the Second Australian Imperial Force as a medical officer with the rank of captain in the 2nd Field Ambulance. He saw service in the Middle East, the Battle of Bardia, the capture of Tobruk, the Greek campaign, the Battle of Crete, New Guinea and Borneo. He was promoted to major in 1942 and later to lieutenant colonel. He was mentioned in despatches four times and was appointed an Officer of the Order of the British Empire in 1944. In Syria, he took charge of a hospital where he treated the local sex workers for sexually transmitted diseases, which caused the incidence of disease amongst the local soldiers to drop.