In 1998, N'Djili airport was the site of one of the decisive battles of the Second Congo War. Rebel forces advancing on Kinshasa infiltrated the airport perimeter but were repulsed by Zimbabwean troops and aircraft arriving to support the government of Laurent Kabila.
The airport has barely been maintained or upgraded and is still using the infrastructure built by the Belgians during the colonial era. Some computerized upgrades to the arrivals terminal have been implemented in recent years and in June 2015 a new international terminal was opened which can service 1 million passengers per year.
On 21 June 2010, Hewa Bora Airways Flight 601, operated by McDonnell Douglas MD-82 9Q-COQ burst a tyre on take-off. Hydraulic systems and port engine were damaged and the nose gear did not lower when the aircraft returned to N'djili. All 110 people on board escaped uninjured. The airline blamed the state of the runway for the accident, but investigators found no fault with the runway.
On 4 April 2011, a Canadair CRJ-100ER 4L-GAE of Georgian Airways operating under an UN mission as flight 834 from Bangoka International Airport, Kisangani to Kinshasa missed the runway on landing at Kinshasa. The aircraft subsequently broke into pieces and caught fire. Only one survivor is reported out of 29 passengers and 4 crew. The airport was experiencing torrential rain, thunderstorms and low visibility at the time.