[3] The airport opened in July 1998, with hours initially limited to 8.30 a.m. to 8 p.m. At the airport's outset, All Nippon Airways operated flights to Tokyo, Osaka and Nagoya and Japan Air System operated a daily flight to Osaka.

By fiscal year 2011, these subsidies totaled 4.2 billion yen, while landing fees payable to the prefecture had been slashed to one-third of their original level.

The prefectural government's 10-year plan calls for adding flights to Hong Kong, Taipei and Southeast Asia, doubling the terminal capacity to two domestic and two international gates, increasing parking and check-in space, and potentially extending the main runway to 2,500 m.[2] As of late 2014, the Ministry of Defense was considering Saga Airport as the primary basing location for the JGSDF's planned fleet of 17 V-22 tiltrotor V/STOL transports.

In the meantime, aircraft of the Japan Self-Defense Forces in general are making increasing use of Saga due to ongoing regional tensions with North Korea.

As of 2023, the JGSDF is planning to base a significant aviation element at the airfield beginning in 2025 for the purpose of better defending Japan's southern Nansei Islands.