The airport was originally built in the 1940s as Sungai Durian Airport. In the 1980s, it was renamed Supadio Airport. Supadio has a history of domestic and limited international flights. In the 1970s flights started to Kuching International Airport by Merpati and, in the 1980s flights to Singapore serviced by Garuda.
Supadio International Airport is going to have new terminal building with its runway to be lengthened and widened, to make it a world-class airport. In 2012 tender to overlay 2,250 meters runway has been done, and in early 2013 overlay will be done. Multiyears project to expand runway to 2,500 meters began in 2013. Before, in 2010–2011 runway has been widened from 30 meters to 45 meters.
The new terminal was now being constructed and expected to be finished totally by 2016. The project would be separated into 2 phase. Phase I involves building a temporary terminal with an area of 13.000 m2 and could accommodate over 1.5 million people over a year. This temporary building would be located adjacent to the existing terminal, Phase 2 involves demolishing of existing terminal building and building a new terminal building as an extension of the building in phase I. In total, the new Supadio Airport terminal would have an area of 32.000 m2 and could accommodate 2.5 million people a year.
On 22 November 2004, Sri Hardono, the captain of Garuda Indonesia flight 501, a Boeing 737-500 from Pontianak to Jakarta, was suddenly ill shortly after take-off. Hardono immediately asked permission to the air traffic control to return to the airport. Hardono died shortly after the emergency landing while still in the cockpit. Heart attack was the cause of illness and death. Due to the incident, the airport was temporarily closed for 40 minutes. There were no other injuries or fatalities in this incident.
On 2 November 2010, Lion Air flight 712, operated by Boeing 737-400 PK-LIQ, overran the runway on landing, coming to rest on its belly. All 174 passengers and crew evacuated by the emergency chutes, with few injuries reported.
On 1 June 2012, a Sriwijaya Air Boeing 737-400 skidded off the runway in heavy rain. Nobody was hurt, but the plane sustained damage beyond repair.