Chowne spent a brief period in the 36th Battalion, a Militia unit, before enlisting in the Second Australian Imperial Force in late May 1940. He was assigned to the 2/13th Battalion as a platoon message runner, and was later made company runner. The unit, part of the 9th Division, arrived in the Middle East in November 1940 and later joined the North African campaign, defending Tobruk for eight months in 1941. During his time at Tobruk, Chowne transferred to the carrier platoon and was promoted to corporal. After Tobruk the 2/13th performed garrison duties in Syria where, in September, Chowne was promoted to sergeant. He was wounded in the leg and hand at El Alamein the following month and spent three weeks in hospital. He returned to Australia with the battalion in January 1943.