On 19 March 2016, the Boeing 737-800 aircraft operating the flight crashed during a go-around, killing all 62 passengers and crew on board.

[7] In 2015, Flydubai passed the safety audit of the IATA, and several days before the crash had become an official member of the organization.

One pilot who told BBC News that staff had insufficient time to rest between shifts also informed senior management, who replied that "we don't have a fatigue issue at Flydubai."

[22][23] An alert from Flight 981's onboard windshear-warning system caused the pilots to abandon their landing approach a few kilometres from the runway.

[1]: 148  This caused the nose to pitch up significantly, and the captain (who was flying the airplane) attempted to counter the force with considerable effort on the control column.

[19] The American team consisted of air-accident investigators from the National Transportation Safety Board, experts from Boeing and representatives of the Federal Aviation Administration.

[29] In a statement, it listed "crew error, technical failure, adverse weather conditions and other factors" as possible reasons for the crash.

Russian and Emirati experts started an analysis of the radar data, flight crew–ATC communications and meteorological information.

[19][needs update] On 21 March 2016, investigators in Rostov-on-Don finished collecting debris from the crash site and started reconstructing the fuselage layout in a hangar.

[19][needs update] On 29 March 2016, the IAC announced that preliminary analysis of information from the flight recorders showed no evidence of the failure of any aircraft systems, engines or other components.

[19] A transcript of more than two hours of the last crew communications was prepared but was not released to the press, as international and Russian rules of air-crash investigation forbid publication.

[31] On 26 November 2019, the IAC published its final report, which stated the cause as a combination of incorrect aircraft configuration, pilot error and the subsequent loss of the pilot-in-command's situational awareness in nighttime storm conditions.

The go-around procedure with retracted landing gear and flaps but with the maximum available thrust consistent with the windshear escape manoeuver, combined with the lightness of the aircraft, led to the excessive nose-up attitude.

[1] In light of the disaster, Rostov Oblast governor Vasily Golubev announced that the government would pay one million rubles (about 15,000 USD) to the families of the victims.

"[36] On 24 March 2016, crown prince of Abu Dhabi Mohammed bin Zayed Al Nahyan travelled to Moscow to discuss the course of the crash investigation with Russian president Vladimir Putin.

The Flight 363 investigation, conducted by the Interstate Aviation Committee, ruled that the 2013 accident was the result of pilot error.

[39] On 28 March 2016, Artyom Kiryanov, a Russian Civic Chamber member, called for Russia's Federal Air Transport Agency and the IAC to suspend the flying certificates of all Russian owned-and-operated Boeing 737 Classics and Next Generation series, until the end of the Flight 981 investigation, citing concerns about the elevator controls in all 737s.

[42][needs update] The crash was featured in season 22, episode 1 of the Canadian documentary series Mayday, titled "Holding Pattern.