Two days after the Japanese attack on the US fleet at Pearl Harbor and the British in Malaya, on 9 December 1941 the battalion was ordered to "prepare to move" as it was mobilised for war service. The threat of invasion by the Japanese changed the strategic situation and with it the planning forecasts of the Australian high command. As such, instead of relieving the 49th Battalion, the 39th was combined with the 49th and the New South Wales-based 53rd Battalion to form the 30th Brigade, and plans were made for the entire formation to deploy to New Guinea. Christmas Day 1941 was spent in camp, before the 39th Battalion was loaded onto two trains the following day for a rapid move north. One train went straight to Albury and the other departed from Spencer Street station, Melbourne, two hours later. Both trains arrived in Sydney at 10:40 hours, on 27 December 1941. The battalion then detrained and moved by ferry to Woolloomooloo Wharf where the 1,068 officers, NCOs and men of the battalion boarded the passenger ship the "Aquitania" bound for New Guinea.