Raised in early 1942 from the remnants of a British unit that had been destroyed in Malaya, the squadron flew Bristol Beauforts from bases in Queensland and New Guinea, undertaking torpedo- and level-bombing sorties against Japanese targets in the Pacific theatre.

[5] Following these attacks the squadron was withdrawn to Laverton in July, subsequently conducting patrols off New South Wales and Victoria and undertaking further training.

100 Squadron struck the mast of the wrecked SS City of Adelaide in Cockle Bay, Magnetic Island.

[8] On 6 October 1942 the Squadron conducted its first torpedo strike, with six Beauforts unsuccessfully targeting Japanese naval vessels.

100 Squadron flew reconnaissance patrols and anti-shipping and bombing missions against the Japanese in the Solomon Islands and New Guinea mainland.

It was not successful in sinking any ships in this battle, though, and from March 1943 it operated solely in the level bombing role.

[10] On 4 October, ten Beauforts made a low-level attack on the Japanese airfield at Gasmata, with three aircraft being shot down.

[11] The squadron bombed a bridge over the Anwek River in November as part of an air offensive over New Britain and the same month moved to Goodenough Island.

100 Squadron conducted missions against Japanese facilities throughout New Guinea and surrounding islands during 1944, including the key base at Rabaul.

[16] The squadron continued in this role until the last day of the war, flying its final bombing mission the morning Japan surrendered, on 15 August 1945.

[18] There it undertook ferrying and courier flights until disbanding on 19 August 1946;[17] prior to this, the squadron's strength had dwindled as personnel were repatriated back to Australia for demobilisation or transferred to other units for subsequent service with the occupation forces in Japan.