Bonaire's first airport was located near Tra'i Montaña near Subi Blanku and crossed the current road from Kralendijk to Rincon. It was only a landing strip and a shelter. It was built in 1936 and is considered the location of the beginning of aviation on Bonaire.

The construction work for this airport began on September 23, 1935. The intention was to make a longer runway, but it proved impossible to construct more than 475 meters because the eastern portion of the land was very low. Part of the field had to be modified, in particular where aircraft met or left the ground during landing and take-off. This area covered more than 100 metres of the runway, and had to be paved with a mixture of sand and stone.

KLM decided on May 9, 1936, to route-test the first flight to Bonaire from Curaçao. The Oriol (Fokker F-XVIII "Snip") was chosen for this test. The first experimental landing was successful and also a historic moment. KLM made the first official flight with passengers on May 31, 1936.

American soldiers arrived on Bonaire in the second half of 1943 and their commander stated that a new airport had to be built. In December 1943, construction began in the vicinity of where the airport is today. The new airport, named "Flamingo Airport", was put into use in 1945. This was a big step forward for Bonaire and its aviation. A small terminal was built that was suitable for the number of passengers at the time. This building was used until 1976.

The construction of a new runway began in the last months of 1953 and was completed in 1955. The small terminal had been extended with a terrace where luggage could be delivered. The runway was extended and expanded several times. In 1960, the runway had a length of 1,430 meters and a width of 30 meters. Hotels and interested parties on the island continued to push for a further extension of the runway so that charter flights from the United States were able to land here. Those flights were typically operated with McDonnell Douglas DC-8 or Boeing 707 aircraft.

In 1970 the runway was extended to a length of 1,750 meters and a width of 30 meters, enough for a McDonnell Douglas DC-9 to land and take off fully loaded. On June 7, 1974, a public tender for the construction of a new terminal building was made. The building became operational in 1976. Meanwhile, hotels and foreign investors continued to insist that the runway be extended further. This was needed before any more hotels could be built. In 1980 the runway was again extended to 2400 meters long and 45 meters wide, and in October 2000 another extension was carried out, resulting in the current runway length of 2,880 meters to facilitate the largest airliners on intercontinental flights.

The Dutch national carrier, KLM, used the airport to refuel planes en route from Amsterdam to Ecuador and Peru, using MD-11 and Boeing 747 between 1997 and 2011.