During World War II the battalion was sent to New Guinea in 1942 as part of the 30th Brigade to defend the territory against a Japanese attack. Subsequently, between July and August of that year the unit was heavily engaged in the defence of Port Moresby, fighting along the Kokoda Track. The 39th fought several desperate actions against the Japanese as they attempted to hold out until further reinforcements could be brought up from Port Moresby. They were also later involved in the fighting around Buna–Gona. Such was their involvement in the battle that by the time they were withdrawn they could only muster 32 men and following its return to Australia, the unit was disbanded in early July 1943.