Ernest Failloubaz, holder of Swiss pilot licence No. 1, flew from Avenches to Payerne in September 1910, and the Confederation leased land from the town in 1921 to build an airfield. The army opened it in 1925, and it grew through the Second World War into the largest military aerodrome on the Swiss plateau. Because Payerne lay outside the Alpine Réduit it was never a cavern base; its protection came from hardened shelters, dispersal and a taxiway link to the A1 motorway, which was built as an emergency runway and was used again for F/A-18 take-offs and landings in June 2024, the first such exercise since the Cold War.

Payerne received the first licence-built Hornets in 1997 with Fliegerstaffel 17 and has been the centre of Swiss fighter aviation ever since. The 24-hour Luftpolizeidienst reached full capability here on 31 December 2020, with two armed F/A-18 held at 15 minutes readiness around the clock. The base employs more than 500 people, trains 32 apprentices a year, hosted the Air04 and Air14 shows and the flight-test phase of the Air2030 competition in 2019, and shares its 2.8 km runway with the civilian Swiss Aeropole park and Solar Impulse.

Under the 2026 army organisation, Fliegerstaffel 17 and 18 were merged into the new Fliegerstaffel 35, which will be the first unit to convert to the F-35A when aircraft arrive from mid-2028. A new maintenance and shelter complex for the Lightning II is under construction, and RUAG moved F/A-18 depot maintenance here in 2021.