During the Falklands War of 1982, the Fleet Air Arm only had three Sea Harrier squadrons, 800 and 801 (with five aircraft each for frontline operations from HMS Hermes and HMS Invincible) and 899 NAS (with around twelve Sea Harriers operating as the headquarters and training squadron). At the outbreak of war, 899 sent three aircraft to join 801 aboard HMS Invincible and seven aircraft to join 800 aboard HMS Hermes. These aircraft sailed with the Task Force whilst the remains of 899 set about bringing the remaining Sea Harriers in store or on other duties into operational use.

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It was planned to form a third frontline sqn with ten Sea Harriers, but only eight could be brought together initially. These aircraft were painted a lighter low visibility grey than the rest of the Sea Harrier fleet, and were then issued to the reformed 809 NAS, under Lt Cdr Tim Gedge, which were transported south on the ill-fated Atlantic Conveyor. After arriving with the Task force, the aircraft and pilots were split between the two carriers and were absorbed by their sqns, as 899's aircraft had been earlier. After the ceasefire, 809 re-formed as a single unit and returned to the UK aboard Hermes, where after a very short break they embarked aboard the newly completed HMS Illustrious and returned to the South Atlantic, remaining on station until relieved by RAF F-4M Phantom FGR2s of 29 Squadron now based at Port Stanley Airport. Illustrious returned home in December, and 809 NAS finally disbanded on 17 December 1982.