In early 1942, the 2/9th was brought back to Australia where it was re-organised for jungle warfare and took part in the New Guinea campaign. Throughout 1942–1944, the battalion was committed twice to the fighting against the Japanese in New Guinea. In 1942–1943, the 2/9th fought actions at Milne Bay and Buna–Gona before being withdrawn to Australia for rest prior to returning to New Guinea to take part in the advance through the Finisterre Range where the battalion took part in the Battle of Shaggy Ridge in 1943–1944. The battalion's final involvement in the war came during the Borneo campaign in mid-1945, when it took part in the landing at Balikpapan. It was disbanded shortly after the war in early 1946.