Bardufoss was selected an emergency landing airfield by the Norwegian Army Air Service in 1934, with construction starting in early 1935. A 200-by-200-meter (660 by 660 ft) area was completed in mid-1936 and tested using a de Havilland Tiger Moth. The Army Air Service decided to expand the airport and built a triangular gravel runway 500-by-400-by-300-meter (1,640 by 1,310 by 980 ft), which became operational from mid-1938. Further expansions were carried out in 1939 and 1940. During the German occupation of Norway the runway was expanded to 1,600 by 80 meters (5,250 by 260 ft) in concrete by the Luftwaffe, and a second runway, 1,850 by 90 meters (6,070 by 300 ft) long, was built at Fossmoen, but never used. The airport was reclaimed by the RNoAF in 1945, who started using a water aerodrome on the lake of Andsvann. A runway extension in 1952 and 1953 to 2,500 meters (8,200 ft) was financed by the North Atlantic Treaty Organization.

A government commission published a report in 1947 which recommended a national plan for civil aviation. It recommended that flights in Northern Norway be carried out using seaplanes, but also noted the possibility of upgrading existing military air stations for civilian use. Scheduled services to Bardufoss started in 1956, with SAS extending its service from Oslo Airport, Fornebu via Trondheim Airport, Værnes to Bodø Airport to Bardufoss. The initial terminal at Bardufoss was half a hangar leased from the air station. Bardufoss was the only land airport north of Bodø and its catchment area included the towns of Tromsø, Harstad and Narvik. Travel time to Narvik was three hours, Harstad was six hours away and Tromsø was 140 kilometers (87 mi) by road. The towns were also served by the coastal seaplane route, but it only operated during the summer. Widerøe launched a seaplane route from the water aerodrome to Tromsø, Alta and Hammerfest. This route lasted until 1963.

Three times a week SAS operated a night flight from Bardufoss and Bodø to Oslo, with Andøya Airport, Andenes added in 1964, using a Convair Metropolitan. A new terminal opened in 1962. Three airports were opened in Finnmark in 1963, Alta Airport, Lakselv Airport, Banak and Kirkenes Airport, Høybuktmoen, and the service from Bardufoss was extended to those towns. Tromsø Airport opened the following year, reducing the number of services to Bardufoss. SAS flew the Sud Aviation Caravelle to Bardufoss for the first time in 1963 and introduced the Douglas DC-7 in 1965.

From 1964 the Norwegian Armed Forces organized its own flights through chartered aircraft. Braathens SAFE received permission in 1967 to extend its West Coast route from Bergen to Trondheim onwards to Bodø, Tromsø and Bardufoss. Widerøe took over some of SAS flights between Bodø, Tromsø, Andenes and Bardufoss in 1971. The terminal was extended in 1972 with a new arrivals hall. SAS introduced a freight aircraft on the route from Oslo to Bodø, Bardufoss and Tromsø from 1982, using a Lockheed L-188 Electra operated by Fred. Olsen Airtransport. The route proved unprofitable and was terminated in 1989. The airport was classified as an international airport until 1985. A new cafeteria opened in the terminal in 1988. The airport served 85,300 passengers in 1990.

The Norwegian Aviation College was established at Bardufoss Airport in 1992 as the world's northernmost flight school. It chose the airport because of its difficult weather and terrain in combination with few aircraft movements from commercial aviation. The use of military charter flights was debated from 1976. While they were cost-efficient for the military, merging them with civilian routes would increase the patronage of scheduled services, which would increase frequency and aircraft size. Coordinate flights were introduced in October 1992 and resulted in three weekly services with SAS to Oslo. A new control tower, costing NOK 55 million, was completed in September 1993. Plans for a new terminal commenced with the coordination of civilian and military flights, which had initially resulted in the old civilian terminal being closed. An early proposal was to build a new arrivals hall and keeping the former military terminal as a departures hall. The airport handled 142,100 passengers in 1997.

The armed forces signed an agreement with Braathens, resulting in the airline taking over the three weekly Oslo-services from 1 January 1999. The airport hit a temporary high 190,000 passengers in 2000, largely because of increased military activity. This dropped to 150,000 in 2003. A new terminal opened on 16 January 2004, costing NOK 5.85 million. Construction took four months and the main contractor, Thor Olsen, built the terminal without profits. The old terminal building was demolished free of charge. SAS and Braathens merged in 2004, creating SAS Braathens.