The county has a long tradition of association with the RAF. There are world-famous bases located throughout the county, many of which served as vital and pivotal centres during recent conflicts from the Great World Wars to more recent operation in the Middle and Far East.

The most famous Lincolnshire Royal Air Force of all, the magnificent Red Arrows - officially known as the RAF Aerobatic Display Team - are based north of Lincoln at the equally famous RAF Scampton, site of a World War I landing field. They are currently the sole flying users of the base. Despite its heritage and use for the modern remake of the original 1954 Dambusters film, it seems likely site will close within the decade seeing the Control and Reporting Centre, the Mobile Met Unit and the Red Arrows relocating.

RAF Cranwell, near Sleaford, is home to Headquarters, Air Cadets, and the Air Cadet Organisation's Adult Training Facility. The main building at Cranwell is noted for its distinctive dome. Cranwell is also home to 3 RAF flying squadrons, No. 16 Elementary Flying Training, No. 55 Weapons Systems Operator training, and No. 45 multi-engined aircraft training. No.3 Flying Training School for navigators and non-commissioned aircrew is also based there, as are two of the RAF’s excellent bands - The Band of the Royal Air Force College and The Band of the Royal Air Force Regiment.

RAF Barkston Heath, a beautifully unspoiled Second World War airfield, acts as a Relief Landing Ground for the flying training activities at RAF Cranwell and is venue for the British National Model Aircraft Championships. RAF Waddington is home to the RAF's Sentry, Nimrod and Raytheon Sentinel ground-surveillance/intelligence aircraft. The station is also home to No. 34 Expeditionary Air Wing. There is an outdoor viewing area close to the northern end of the long runway, itself originally designed to accommodate V-bombers. The base is home to the RAF’s largest display event, the annual Waddington International Air Show.

RAF Digby serves as the headquarters of the Joint Service Signals Organisation, and is the oldest station in the RAF. RAF Digby contains personnel from all three of the British Armed Forces and allied forces. It contains four operational units: HQ Joint Service Signals, Signal Unit, 591 Signals and the Aerial Erector School. More recently, the station has hosted a new annual RAF-established event open to the public, Party in the Park, now a regular fixture in late July or early August. RAF Coningsby is home of the Operational Evaluational Unit, the Operational Conversion Unit and the first Typhoon Operational Squadron, flying the Eurofighter Typhoon. Also based at Coningsby is the RAF's Fast Jet and Weapons Operational Evaluation Unit.

RAF Donna Nook , just north of North Somercotes is the only National Nature Reserve in the UK on MOD land. It has a large seal habitat maintained by the Lincolnshire Wildlife Trust. RAF Holbeach and RAF Wainfleet are Royal Air Force bombing ranges situated between Boston and Kings Lynn on The Wash. The ranges provide facilities for RAF and other NATO aircraft to practice dropping bombs and firing their cannon. Targets include several old trawlers which have been beached on the sands of The Wash for this purpose. RAF Holbeach also has facilities for scoring strafing runs.