Malakal Airport sits at 1,291 feet above sea level on the west side of the White Nile, just north of Malakal's central business district and next to the main campus of Upper Nile University. Runway 05/23 is 2,000 meters long, paved, and long enough for regional jets and most UN aircraft. It is the smaller of South Sudan's two international airports; Juba International Airport lies 521 kilometers to the south. During the Second Sudanese Civil War and again during the South Sudanese civil wars that followed independence, Malakal became one of the most important humanitarian airports in East Africa. UN Operation Lifeline Sudan and its successors flew food, medicine, and staff in and out of here for decades. The United Nations Mission in Sudan, and later the United Nations Mission in South Sudan (UNMISS), have used the airport as a logistics hub.

The airport has been damaged, repaired, overrun, and rebuilt in step with the city it serves. Between 2013 and 2015, during the worst of the Second South Sudanese Civil War, Malakal changed hands twelve times between government SPLA forces and opposition-aligned fighters. The BBC described it in 2015 as 'the city that vanished,' because whole neighborhoods had been reduced to rubble. The airport, protected by UN troops and strategically necessary to all factions, kept functioning through the worst of it. Passengers on humanitarian charters sometimes looked out over wreckage on final approach. Aid workers flew in carrying laptops and flew out carrying malnourished children for medical evacuation. The airport's staff (ground crews, refuelers, radio operators) kept showing up to work at a runway surrounded by a war.

Aviation safety here has always been fragile. On November 10, 2015, a Hawker Siddeley Andover (registration TL-AEW) of the Central African Republic impacted a field and burned shortly after takeoff. All four crew members survived, but the aircraft was consumed by fire. In 2024 three incidents occurred in quick succession. On February 9, an African Express Airways MD-82 (5Y-AXL) suffered a main-gear collapse and belly-landed short of the runway with no injuries. On March 31, a Safe Air Boeing 727-200 freighter (5Y-IRE) collided with that wreckage while attempting to land. On August 9 a Renegade Air Dash 8-300 (5Y-SMI), contracted to UN Humanitarian Air Service, lost its landing gear wheels during takeoff from Maban and made a gear-up landing at Malakal with all 35 people aboard surviving. Four aircraft bent out of shape in a single year. In a country whose aviation infrastructure is stretched thin and whose alternative transport options are mostly non-existent, every incident of this kind closes a window of possibility for a region that cannot afford closed windows.

For the people of Malakal, the airport is not primarily a convenience. It is a medical evacuation vector when the hospital cannot cope. It is a way for family members to reach Juba, Nairobi, Khartoum. It is how food arrives when the White Nile barges are interdicted and the roads are impassable. The airport is also how journalists fly in to tell the world what is happening in Upper Nile State, and how diplomats arrive to talk about peace agreements that will eventually be broken and then negotiated again. The arrivals hall is small, hot, noisy. The departures lounge is smaller. Passengers sit on benches under ceiling fans and wait, and their waiting is for aircraft that may or may not arrive depending on weather, fuel, security, and the dozen other variables that determine whether flight is possible on a given day in a country that is still putting itself together.