On April 1, 1960, Kumamoto Airport commenced its services as a second class airport with a 1,200m x 30m runway in a part of the old airport site for the Imperial Japanese Army, located approximately 7 km east of central Kumamoto City. Subsequently, to meet the rapidly increasing demands for air travel, a plan to extend its runway to 2,000m was firstly discussed. However, due to the difficulty in purchasing land and noise pollution problems it could cause, the plan was reformulated based on the decision to relocate the airport. In 1966, Takayubaru Plateau was chosen as a site for new Kumamoto Airport after implementing flight and meteorological investigations.

It was decided that the construction of the airport would be implemented according to the first five-year plan commencing in 1967. During the construction, the runway was extended to 2,500m, 500m longer than the original plan, as there were requests from Kumamoto Prefectural Office and a prospect of flight services by larger aircrafts. On April 1, 1960, new Kumamoto Airport had its grand opening.

Furthermore, as the 500m extension was decided in the third five-year plan, it commenced its services with the 3,000m runway in April 1980.

Since its opening, the improvement of actual operation rates has been a vital issue as the airport is located on a plateau at 193m elevation where dense fog is likely to come down. To solve this issue, upgrading of the airport such as instrument landing system (ILS) and airfield lighting system had been implemented from 1991. In September 1995, Category III of ILS, capable of providing guidance along the runway surface with a low visibility, was introduced for the first time in Japan and dramatically improved the actual operation rates and punctuality.

In June 1975, the airport was designated as a specified airport based on so-called Law Concerning Prevention of Disturbance from Aircraft Noise and implements the measures to prevent noise pollutions caused by aircrafts.