Since its formation elements of the regiment have made operational deployments to Cambodia, Papua New Guinea, East Timor, Iraq, Indonesia and Pakistan.

The aircraft were painted in UN white and fitted with armour plating and door mounted machine-guns for the operation due to the threat of ground fire.

They were subsequently used to resupply UN positions along the Thai-Laos border, as well as the transportation of electoral officials and ballot boxes, and for aeromedical evacuation.

By 2004 the regiment provided a 24-hour aeromedical evacuation capability in support of the Australian infantry battalion deployed along the East Timor-Indonesian border, as well as the insertion and extraction of reaction forces.

[6] Two years after being withdrawn, eight Black Hawks were deployed to East Timor in May 2006 as part of Operation Astute as a result of the deteriorating situation in the country.

[9] The aircraft was conducting a re-supply mission in company with a US Army Chinook in Zabul Province when it crashed, injuring six personnel on board.

The helicopter, a CH-47D (ADF serial A15-102) attached to the US Army 159th Combat Aviation Brigade at Kandahar, was assessed as being unrecoverable and was subsequently destroyed at the site of the crash.

[15] In 2016, NH90s from A Squadron deployed on HMAS Canberra to Fiji[16] to provide disaster relief following Tropical Cyclone Winston.

In late 2019 and the beginning of 2020, 5th Aviation Regiment deployed throughout Eastern Australia to assist the civil authority in response to the 2019–20 Australian bushfire season.

[20] One of the regiment's helicopters started what developed into a major bushfire near Canberra when its landing light ignited dry grass.

[22] In early 2021, A Squadron MRH90 returned to Fiji in the wake of Cyclone Yasa and 'flew more than 166 hours, delivering 71,475kg of aid through 62 vertical replenishments, as well as troops, to communities across Vanua Levu and outlying islands'.

[24] The regiment was subsequently expanded in 1995 when 'C' Squadron was formed to operate CH-47 Chinook and UH-1 Iroquois helicopters (the later in the aerial fire support role).

[27] In July 2021, the first two Chinooks of an additional four that were purchased were air-delivered from the United States in a C-5 Galaxy 'as part of a half-billion-dollar boost to its fleet of heavy-lift helicopters'.

These helicopters will be based at Oakey, Queensland and Holsworthy, New South Wales, with the 5th Aviation Regiment's two current Taipan-equipped squadrons relocating from Townsville.