Raised in August 1941, it operated PBY Catalina and Short Empire flying boats from bases in New Guinea, Queensland and the Northern Territory, conducting search-and-rescue, mine-laying, anti-submarine and bombing missions against Japanese targets in the Pacific theatre.

[2][3] The squadron conducted long-range patrols between bases scattered around the islands to Australia's north in conjunction with No.

[2][6] The squadron undertook its first sortie of the Pacific War on 8 December; a Catalina located three Japanese luggers in the vicinity of Thursday Island, Queensland.

[2][7] Later in the month it commenced anti-submarine patrols and, in January 1942, bombing raids against Japanese bases.

[4][8] On 21 January, one of its Catalinas located the Japanese fleet steaming for Rabaul and signalled a warning to the town's Australian defenders before being shot down by anti-aircraft fire; it was the squadron's first combat loss.

[10] Their raids on Rabaul did little to stem the Japanese advance, and in the following months Port Moresby itself was subjected to increasingly frequent attacks, which destroyed aircraft, facilities, and squadron records.

On 27 June, each squadron contributed an aircraft to a four-hour raid over Lae and Salamaua during which, as well as bombs, the RAAF crews dropped beer bottles to disrupt the enemy soldiers' sleep—the sound they made falling through the air was, according to the official history, "something between a shrill whistle and a scream".

[17] Its prime responsibility in early 1942 was maritime reconnaissance as far as New Guinea, the Solomon Islands, and New Caledonia; the latter half of the year saw a greater focus on night bombing.

[2][18] From Cairns it continued to conduct reconnaissance, anti-submarine and occasional bombing operations over the waters around New Guinea.

[19] The squadron's role changed in June 1943 when it commenced mine-laying operations over the Netherlands East Indies and the Philippines, though it continued to make some bombing raids and supply drops.

20 Squadron was shot down while attacking a ship at Pomelaa in the Dutch East Indies; the loss was compounded by the fact that one of the coordinators of the mining campaign, Lieutenant Commander P.E.

[23] Another of the squadron's Catalinas went down on the night of 27/28 January 1945, possibly in a cyclone over the Timor Sea, during the campaign to mine Surabaya.

20 Squadron's Catalinas was lost on the night of 7/8 March, most likely owing to bad weather rather than enemy action.

20 Squadron flew its last mission, a transport flight to Balikpapan, on 21 January 1946, and disbanded at Rathmines on 27 March.

20 Squadron was reactivated on 1 April 2015 to support airfield operations at RAAF Base Woomera, South Australia.

[28][29] The design of the reactivated squadron's crest includes a wedge-tailed eagle to denote courage and nobility, a woomera spear thrower to symbolise the town and its indigenous heritage, Sturt's Desert Pea to represent South Australia, and the Pleiades star cluster, which features in the folklore of the local Kokatha people.