In 1937, he met his future wife Helen Ferguson. Since she a student he went to England to take up postgraduate studies. When World War II broke out Dunlop became a specialist surgeon to the Emergency Medical Services. He then enlisted in the Australian Army Medical Corps, rising to the rank of Lieutenant Colonel. While Dunlop was in the Middle East, Helen joined him and they became engaged. In 1943, Ernest became imprisoned in Singapore. He was then sent to Thailand by the Japanese. In Thailand he worked at the Burma Railway as a medical officer. After the war he got married.