The airline was established on 20 June 1967 as Southwest Air Lines (南西航空, Nansei Kōkū), and started operations in July 1967.

It had 814 employees (in March 2023) and is owned by Japan Airlines (51.1%), Naha Airport Terminal (17%), Okinawa Prefecture (12.9%) and others (19.1%)[4] It flew Convair 240s until new capital from JAL allowed it to upgrade to NAMC YS-11s, and eventually Boeing 737s.

JTA occasionally lends aircraft to JAL in the event of equipment failure.

JTA also provides maintenance services for JAL Group Boeing 737-400 aircraft.

At one time the head office of Southwest Air Lines was at 306-1 Kagamizu in Naha.