Svartnes was constructed by the Luftwaffe during the German occupation of Norway during World War II. The background for the establishment was Soviet attacks on supply convoys operating to Kirkenes. During construction, on 12 July 1943, eight Soviet Ilyushin Il-2s attacked Svartnes, but all were shot down. While the war remained in the area Soviet air attacks continued on the air base. The airport was completed in the fall of 1943, it was exclusively used for fighter aircraft detachments of Jagdgeschwader 5. These were used as part of the defense of German ship traffic around Varangerhalvøya. The original wooden runway was 1,000 by 90 meters (3,280 by 300 ft). The Wehrmacht operated a prisoner of war camp at the military base. The air base fell into disuse following the German evacuation in 1944.

The wooden runway was pillaged by locals to accumulate building materials for reconstruction. The Norwegian Armed Forces established itself in Vardø in the mid-1950s. The airport was renovated; a terminal was built consisting of two simple barracks, one used as a passenger terminal and the other as a tower, consisting of a glass addition on the roof. The 1,100-by-80-meter (3,610 by 260 ft) gravel runway received portable runway lights. The Royal Norwegian Air Force served the airport with de Havilland Canada Twin Otter and Shorts Skyvan aircraft to transport military personnel.

The first plans for a civilian airport at Svartnes was launched by Varangfly, later renamed Norving, in 1964. Vardø was mentioned as one of five villages in Finnmark which the airline hoped to open with simple airfields which could serve air taxi and air ambulance flights. Two years later several major airlines proposed a network of short take-off and landing (STOL) airports in Northern Norway, and Vardø was proposed as a possible location. A county committee was established in 1966 to look into the matter. It considered seven locations in Finnmark, including Vardø and recommended in its report that planning continue. Simultaneously the Ministry of Transport and Communications was working on a plan for larger short take-off and landing airports. It decided that such airports will first be built in Helgeland, then Lofoten and Vesterålen and finally in Troms and Finnmark.

Norving started operating irregular air taxi flights to Vardø after they took delivery of an eight-seat Britten-Norman Islander in April 1970. In addition, the airline used the air field for air ambulance services. Norving received permission to operate a scheduled taxi route from Vardø to Kirkenes Airport, Høybuktmoen and Båtsfjord Airport from the late 1970s.

Construction of a new terminal and upgrading the airport to regional standard started in 1984. In February 1987 Vardø Municipality received operating permission from the government. The investments cost NOK 11.4 million, of which NOK 10 million was to be financed through a loan and the rest through subsidies from the government and the county. The latter was also responsible for covering the operating deficit. The upgraded airport opened on 6 April 1987. The first two months Norving continued its taxi route service to the airport, but from 1 June a regular concession scheduled service was introduced. Widerøe took over the services in 1991. At first the airport was served using Twin Otters, but from the mid-1990s the Dash 8 was introduced. From 1996, Svartnes and 25 other regional airports were taken over by the state and the Civil Aviation Administration (later renamed Avinor). Widerøe lost the bid to operate the services between 2000 and 2003 to Arctic Air, but resumed services in 2003. Airport security was introduced on 1 January 2005. There has several times been discuss whether to close down the airport, having in mind that Vadsø Airport is 67 km away by road. In 2002 there was political support in Stortinget to close it if the road was upgraded, but neither happened. In 2015 Avinor stated that closing Vardø would give least passenger trouble related to the financial support in the country, but that no decision on it would be made before 2019. Because of lack of available aircraft for purchase, before 2030 all short airports must be extended, closed or be flown with very small planes. Vardø has no room for extension.