The battalion was assigned to the 11th Brigade at this time and used in various garrison roles in the early part of World War II before a detachment was sent to the Dutch East Indies as part of Merauke Force in 1943. Later in the war, the entire 26th Battalion, along with the rest of the 11th Brigade, was committed to the Bougainville campaign where they saw action against the Japanese from late 1944 until the end of hostilities in August 1945. After the war, the 26th Battalion was used to guard Japanese prisoners on Rabaul, remaining there until March 1946, before returning to Australia for demobilisation. It was subsequently disbanded in August 1946.