The military flying units share Aldergrove's runways with Belfast International Airport, but have their own separate facilities and helipad.

Various squadrons were posted here during this time: Aldergrove's location made it an important station of RAF Coastal Command in the Battle of the Atlantic, during the Second World War.

18 Squadron RAF also operated detachments of Boeing Chinook during the late 80s in support of the British Army in Northern Ireland.

The following units were here at some point:[36] The Army Air Corps also operated Westland Lynx and Westland Gazelle helicopters as well as de Havilland Canada DHC-2 Beaver aircraft in its joint operations with the RAF's Reconnaissance Intelligence Centre (Northern Ireland); the Beaver was replaced by the Britten-Norman Islander late in 1988.

The 17/21st Lancers Air Squadron based at RAF Aldergrove from 1969 to 1971 operating with Sioux Helicopters and a Fixed Wing Beaver aircraft.

655 Squadron AAC moved from RAF Ballykelly to Aldergrove with the Westland Lynx AH Mk 7 helicopter.

[31] On 4 August 2008, 651 Squadron Army Air Corps moved back to Northern Ireland from RAF Odiham almost 50 years after its first deployment there.

The base was no longer therefore administered by the JHC and on 1 Apr 2013 became Aldergrove Flying Station under command of 38 (Irish) Brigade.