Previously Stornoway Airport with grass strip runways laid across a golf course in 1939, the site was taken over by Coastal Command and used during 1940-41 without development. The station opened officially in April 1941, when three tarmac-surface hard runways were being laid. Other improvements continued into 1942, including the erection of 10 hangars. Occupied by the RAF until 1946, use of the station as a trans-Atlantic staging post by USAAF aircraft began in July 1942. By June 1943, such transit movements had increased to the point that the station became home to a handling unit of about 100 USAAF personnel. In June 1943 alone, 68 American aircraft passed through on delivery. The USAAF also began in July 1943 a meteorological shuttle service between Iceland, Stornoway and RAF Prestwick. A total of 108 US aircraft of various types passed through the station in September 1943, and it was transferred temporarily to RAF Transport Command in November 1943. However, its primary purpose during 1944-45 was as a Coastal Command base for RAF anti-submarine and anti-shipping patrols. Again a civil Airport from 1946, but with an RAF presence until 1998, it was upgraded in the early 1980s with runway and taxiway extensions, plus new hangars. During the Cold War era, the Airport was used as a NATO Forward Operating Base.

Stornoway today is one of the 11 Scottish airports operated by Highland and Islands Airports Ltd.