The airport was opened on May 16, 1962 for military and domestic civilian use. Prior to this time, Hualien was a military gravel airfield.
On August 24, 1999, a Uni Air MD-90 flight from Taipei carrying 96 passengers and crew exploded just after it landed at Hualien. The blast injured 28 people and killed one, although a pregnant woman miscarried days later. An investigation revealed that former Taiwanese decathlete Ku Chin-shui (), who was not aboard the flight, had given bottles of flammable liquid to his nephew to transport. Ku was convicted in 2002 and sentenced to seven and a half years in prison, but a later trial upon his appeal found him not guilty on December 27, 2004.