The first Kumamoto Airport opened in 1960 on the site of a former Imperial Japanese Army air base and had a 1,200 m runway. It was replaced by the current Kumamoto Airport in 1971. The new airport's 2,500 m runway was extended to 3,000 m in 1980.
Kumamoto was one of three nationally-owned airports to turn a profit in fiscal year 2011 (along with New Chitose Airport and Komatsu Airport). In 2013, the government passed legislation aimed at eventually allowing the sale of an operating concession at the airport.