The squadron was formed in 1939 and saw combat in the South West Pacific theatre of World War II.

The squadron was initially equipped with four Hawker Demon biplane fighters and four Avro Anson maritime reconnaissance aircraft and commenced intensive training in May.

[1] The squadron was the first RAAF unit to be permanently based in the Northern Territory and was initially stationed at Darwin's civil aerodrome.

12 Squadron Ansons were based in Darwin by late August, and these began flying reconnaissance patrols on the last day of the month.

The squadron also lost a considerable portion of its stores when a new hangar was destroyed at the civil aerodrome in this raid.

12 Squadron's surviving aircraft dropped supplies to the survivors of sunken ships and conducted patrols of the area around Darwin.

The only exception to this was a bombing raid conducted on 18 June 1943 by twelve of the squadron's Vengeances against villages on Selaru in the Tanimbar Islands which were believed to house workers employed by the Japanese to build a new airstrip.

The squadron's 270-man strong advance party arrived in Merauke on 8 July but found that no facilities had been constructed for the unit.

As a result, its aircraft were stationed at Cooktown, Queensland, where they were used for anti-submarine patrols and the escort of shipping.

12 Squadron gradually moved to Merauke between September and November 1943, and continued to be employed mainly in maritime patrols.

The squadron's only contact with the Japanese during its period at Merauke took place on 9 October when a Vengeance unsuccessfully attacked a float plane.

12 Squadron moved to Strathpine, Queensland, where it was reduced to cadre status ahead of being converted to a heavy bomber unit.

[7] The squadron moved to Cecil Plains in December and began to be reequipped with Consolidated B-24 Liberator heavy bombers on 5 February 1945.

It flew its first heavy bomber operation on 24 May and attacked three Japanese ships on 26 May, setting one of them on fire.

12 Squadron's aircrew moved to RAAF Base East Sale to begin conversion training for Avro Lincoln heavy bombers.

The helicopters were shipped from the United States to Brisbane on board the aircraft carrier HMAS Melbourne, and arrived in Australia in March 1974.

[19] The squadron made its first flight in the aircraft on 8 July 1974, and was declared operational with the type in December that year.

[19][20] Unusual tasks included placing lighthouses in isolated locations and air conditioning plants on the roofs of tall buildings and supporting police anti-narcotics operations.

[21] Due to the need to reduce defence expenditure, the Australian government decided to retire the Chinook helicopters in 1989.