18 (Netherlands East Indies) Squadron RAAF was formed at Fairbairn on 4 April 1942, paving the way for other such units.

18 (NEI) Sqn was drawn initially from two groups of ethnic Dutch and Indonesian personnel, who had been evacuated from Japanese occupied Indonesia to either RAAF Archerfield, Queensland or Melbourne.

After it had become fully operational with North American B-25 Mitchells, 18 (NEI) RAAF was deployed to, and carried out missions throughout the South West Pacific theatre.

34 Squadron RAAF, which is responsible for the operations of the RAAF's VIP transport aircraft that are used to transport Australian officials such as the Prime Minister, cabinet ministers, the Governor General, the leader of the opposition and high ranking defence force officers when travelling both internationally or within Australia.

Besides being the home base of No 34 Squadron's special purpose VIP BBJ1s and Bombardier Challenger 604s, Fairbairn is also regularly used by other defence force aircraft.

The Therapeutic Goods Administration proposed to relocate its offices and laboratories to Fairbairn from a site in Symonston of which it had been a tenant since 1992 in 2020.