Initially, the 29th Brigade was attached to the 5th Division and undertook garrison duties around Townsville in 1942 before deploying to Milne Bay in early 1943 to garrison Goodenough Island. They later took part in the landings at Tambu Bay before participating in the Salamaua–Lae campaign, helping to capture Lae from the Japanese. Finally, in 1944, after 18 months of service overseas the 47th Battalion returned to Australia with the rest of the brigade for training and reorganisation around Strathpine. It was around this time that the Australian Army began converting a number of its divisions over to the Jungle divisional establishment, including the units of the Militia 3rd and 5th Divisions. The battalion's final involvement in the war came when the 29th Brigade was transferred to the 3rd Division and sent to Bougainville in late 1944. On Bougainville the Australians had launched an aggressive campaign against the 40,000 Japanese on the island. The Australian campaign on the island developed into three separate drives in the north, south and central sectors. In December 1944, the 47th Battalion was assigned to the southern sector, taking part in the 29th Brigade's advance from the Jaba River to Mawaraka. After this they were moved to the rear at Torokina for rest before returning to the take part in a second operation in July 1945 which saw them relieve the 15th Brigade and take part in the advance across the Mivo River.