Flight 538 took off from Jakarta at around 5:00 pm, carrying a total of 146 passengers and seven crew members. Most of the passengers were members of the Nahdlatul Ulama, who were attending a national meeting held after the victorious result of the 2004 Indonesian Presidential Election. The flight was uneventful until its landing.

The flight arrived at the airport during dusk, around 6:00 pm in heavy rain. A thunderstorm was reportedly present during the landing.

Flight 538 was configured appropriately for landing, touched down "smoothly" according to most passengers, and the thrust reversers were deployed. The aircraft, however, failed to slow adequately, overran the runway, and slammed into an embankment. The impact caused the floor of the front portion of the plane to collapse, reportedly killing many of the passengers. The aircraft split into two sections, coming to rest in the end of the runway, and fuel began to leak. Passengers had difficulty locating emergency exits in the waning light. Some of the passengers self-evacuated through the opening in the fuselage.