After the start of World War II, he enlisted in the Second Australian Imperial Force in November 1941 in the artillery. He was sent to Warwick Farm, then on the western outskirts of Sydney, for training. A non-conformist known for being forthright, Fingleton did not enjoy military discipline. In May 1942, he went AWOL from his post at Double Bay on the shores of Sydney Harbour to visit his wife. As a result, he was missing when a Japanese midget submarine launched an attack in the harbour. Soon after, he was deployed to Townsville in northern Queensland in anticipation of a Japanese land invasion, which never materialised. He was then transferred to the Press Relations unit. There he did work in intelligence analysis and censorship.