It operated scheduled passenger services to regional domestic destinations in Japan, as well as some low-demand flights for JAL under wet-lease agreement.

On July 1, 1998, JAL Express commenced operations from Osaka to Miyazaki and Kagoshima with two Boeing 737-400s, non-Japanese cockpit crew, and short-term contracted cabin attendants.

[4] The airline celebrated its one millionth passenger in June 2000 and commenced wet-lease operation for its parent JAL in December 2000.

JAL Express became an affiliate member of Oneworld on April 1, 2007, together with four of its sister airlines, in the alliance's biggest expansion in its young history.

[2][6] JAL Express welcomed the arrival of the new Boeing 737-800 to its fleet in January 2008 and celebrated the tenth anniversary of its first flight in July 2008.

On July 9, 2010, JAL Express pilot Ari Fuji became its first female airline flight captain.