The airline was established on 12 October 1998 and started operations on 23 March 2000, with services from Amakusa to Fukuoka and Kumamoto. It is owned by the municipal government (80% stake) and Japan Airlines. On 1 October 2004, it began service between Kumamoto and Matsuyama. On 18 April 2006, it cumulatively carried over 50,000 passengers. On 1 September 2008, it stopped the service between Kumamoto and Matsuyama. Three days later, on 4 September, it began the service between Kumamoto and Kobe. On 31 March 2010, it stopped the service between Kumamoto and Kobe.
In 2015, Amakusa has been reported that the fleet was 1 of 2 ATR 42-600 with another 3 options has been delivered while the Dash 8 has been transferred to Oriental Air Bridge. Amakusa in the future can fly between Amakusa and Kagoshima, Amakusa and Miyazaki, Amakusa and Kochi, Oita and Osaka, Fukuoka and Osaka, Hiroshima and Osaka as well as Fukuoka and Tsushima.