Kinmen Airport was originally established in 1949 in Sihung Village. In June 1951, the Ministry of National Defense ratified TransAsia Airways to launch its first flight to Kinmen and a once-a-week scheduled flight began to operate. On 23 August 1958, the flight was cancelled due to Second Taiwan Strait Crisis with the People's Liberation Army (PLA). The airport was then moved to Shang-i where it is now located, taken over by the Republic of China Air Force (ROCAF) in consideration of the war with PLA.

With the growing number of passengers traveling between Taiwan Island and Kinmen, the government started to reestablish the civilian flight between the two and it began operation in September 1987 by Far Eastern Air Transport, sharing the same apron and terminal building with ROCAF at the airport. Since then, the new era of civilian flight to Kinmen began. Many other airlines joined the flight route.

Taking the necessary steps to accommodate the passenger growth to Kinmen, the Civil Aeronautics Administration (CAA) coordinated with the government for general construction plan of NT$1.5 billion and built a new civilian airport at the northeastern side of the military airport. On 1 March 1994, the Kinmen Civil Airport was formally established, aiming at providing much more safety, convenience and comfort for the passengers and promoting the progress and prosperity of Kinmen. On 3 March 2000, the CAA implemented improvements of facilities, flight security and quality of service at the airport.