The airport's Wikipedia page makes it sound British, and in one sense it was. The field was originally a Royal Air Force airstrip called Gordon's Tree, named for the 1885 death of General Charles Gordon inside besieged Khartoum, and by January 1940 No. 223 Squadron RAF was operating from it. The area came to be known as El Shajjara, Arabic for the Tree. By January 1942 No. 71 Operational Training Unit was working the field, flying Curtiss Tomahawks and Vickers Wellesleys. Reportedly the OTU had at one point 50 Harvards and 20 Hurricanes on strength. Sudanese independence came on 1 January 1956, and the last RAF unit at Khartoum, No. 8 Squadron, stayed until July 1956. What had started as a Commonwealth training field became the flag carrier of an independent African nation.

A new Khartoum International Airport has been planned for years south of the center of Khartoum, in Omdurman 40 km away. Design targets are ambitious: two 4,000-meter runways, an 86,000-square-meter passenger terminal, a 300-room international hotel. Construction by China Harbour Engineering was supposed to move the airport out of the city it had outgrown. On 4 March 2021 the existing airport's ICAO code was changed from HSSS to HSSK, possibly to pave the way for the new airport to inherit the HSSS code. The transition has not happened. The war came before the new airport did.

The first day of the Sudanese civil war opened at the airport. Rapid Support Forces paramilitaries attacked key installations across Khartoum, and Khartoum International was near the top of their target list. A Saudia airliner that was arriving from elsewhere came under fire; no passengers or crew were reported hurt. Two civilians were killed in separate incidents inside the airport complex. Twenty aircraft on the tarmac were destroyed, including a Saudia Airbus A330 (HZ-AQ30) and a SkyUp Airlines Boeing 737-800. No passenger casualties were reported from the planes themselves, a small piece of luck in what was otherwise a catastrophic opening for civil aviation in the country. The RSF held the airport for two years. The Sudanese Armed Forces attacked repeatedly during the long Battle of Khartoum, and finally retook control on 26 March 2025.

Civil aviation at Khartoum had its rougher moments long before 2023. On 19 July 1983 a Chevron Oil Douglas C-47A crashed after takeoff, both engines failing likely due to contaminated fuel; all 27 aboard survived. The worst incident was Sudan Airways Flight 109 on 10 June 2008. The aircraft, arriving from Amman, ran off the end of the runway. The right engine caught fire and the fire spread fast through the cabin. Preliminary reports claimed 100 of the 200 passengers had been killed; the number was later revised to 30 dead and 184 survivors. Three weeks later, on 30 June 2008, an Ilyushin Il-76 exploded on takeoff at Khartoum; all four crew were killed. On 3 October 2018 two Sudan Air Force Antonovs, an An-32 and an An-30, collided on the ground. Aviation safety is a global problem; Khartoum's record was neither exceptional nor trivial.

Reopening Khartoum International after March 2025 was not a simple matter of clearing rubble. The RSF, having lost the airport, shifted to drone warfare, which does not need to occupy a target to damage it. Three consecutive days of drone strikes, 21, 22, and 23 October 2025, bracketed Badr Airlines's return flight. The airport reopened for domestic flights only, connecting Khartoum with Port Sudan on the Red Sea, which had served as Sudan's de facto wartime capital. International flights remained suspended into 2026, but the ability to move people between two Sudanese cities mattered enormously for aid, family reunifications, and the basic fact of a capital still functioning. The airport hosts a major Sudanese Air Force transport squadron whose aircraft, Antonov An-12s through An-72s, Lockheed C-130Hs, Ilyushin Il-62M and Il-76TD, Dassault Falcon 50 and 900 VIP transports, have flown throughout the war as military necessities have required. The Police Air Wing runs Mil Mi-8s and Mi-17s from the same base. Civil aviation's return, however limited, is a marker of a capital trying to function again.