Skeabrae had an unusual start to its life as the site was originally planned as an early naval airfield, complete with four runways, before being switched to Air Ministry supervision for RAF use. The airfield began to open in August 1940 with the primary aim of providing vital fighter defence for the Royal Navy fleet at Scapa Flow. It was however not until October that the first aircraft arrived, Fleet Air Arm Gloster Sea Gladiators and Grumman Martlets of 804 Squadron. A Martlet from this squadron was the first American built fighter to destroy an enemy aircraft in the Second World War on 25 December 1940.

Hawker Hurricanes arrived in January 1941, firstly from No 3 Squadron before being replaced by No 253 Squadron and subsequently the Norwegians of No 331 Squadron. Supermarine Spitfires were used by various squadrons at Skeabrae from 1942 and fighters continued to operate from the airfield until the end of the war. They were joined latterly by some FAA units such as Nos 801 and 880 Squadrons operating Supermarine Seafires. Fighter training also took place at Skeabrae with No 1491 (Fighter) Gunnery Flight, an aerial target towing unit, moving to the airfield at the end of 1942 and staying to August 1943. In addition to fighters, No 1476 (Advanced Ship Recognition) Flight formed at Skeabrae in early 1943, giving instruction for the bombing of moving targets and ship reconnaissance until disbanding at the start of 1944.

The airfield closed on 1 September 1946 after a short period of Care and Maintenance from the autumn of 1945. Skeabrae was finally relinquished in 1957 after being administered since 1947 by the Royal Navy. It was suggested that the airfield could be merged with Twatt to form a large NATO base but Iceland was chosen as a location instead.

Skeabrae was equipped with various hangars and support buildings. Many of these survived until the 1970s and 1980s before larger scale demolition was carried out. The control tower for example was demolished in February 1990. The former cinema/gymnasium and the bomb store are two of the airfield’s few remaining standing buildings but the runways have almost entirely been removed.