Bonython attended St Peter's College, Adelaide, and upon completion entered into accountancy on the recommendation of his older half-brother John. The Second World War interrupted this: in 1940 he began training as a pilot for the Royal Australian Air Force (RAAF). Bonython served in the (then) Netherlands East Indies and New Guinea, experiencing several "death defying" near misses. He was in hospital in Darwin (with dengue fever) during the 1942 bombing - he had just evacuated and taken cover when the ward he had been in took a direct hit. During his time with the RAAF, Bonython filled the roles of aircraft captain in 1941, and chief flying instructor with the rank of squadron leader in 1943.