The airport has been shut since fighting erupted in April 2023 between the Sudanese army and the paramilitary Rapid Support Forces (RSF), leaving vital infrastructure across the capital heavily damaged.
Witnesses told AFP they heard the sounds of drones in central and southern Khartoum and multiple explosions in the airport area from 4 am until 6 am local time (0200-0400 GMT).
One eyewitness in the Al-Azhari neighbourhood in southern Khartoum said he "heard the sound of an explosion and then a drone passed overhead".
A resident in central Khartoum said he was woken "at 4 am to the sound of drones in the sky. Shortly after, we heard loud explosions in the direction of the airport".
The facility appeared intact during a visit later that day by army chief Abdel Fattah al-Burhan.
Speaking from inside the airport, Burhan said the army was "determined to crush this rebellion" -- a reference to the RSF led by his former ally Mohamed Hamdan Daglo.
On Monday, Sudan's Civil Aviation Authority had said the airport would reopen on Wednesday, with domestic flights resuming gradually after technical and operational preparations were completed.
Khartoum has remained relatively calm since the army reclaimed control earlier this year but drone attacks have continued, with the RSF repeatedly accused of targeting military and civilian infrastructure.
Another eyewitness also told AFP that "drones bombed northern Omdurman", part of greater Khartoum, early Tuesday, an area known to host some of Sudan's largest military installations.
"I saw three drones heading north towards Wadi Sayedna (military) base and I heard the sound of explosions," they said.
There was no immediate claim of responsibility for the strikes.
Tuesday's strike marks the third drone attack on the capital in a week. Last week, drones targeted Khartoum on two consecutive days, including strikes on two army bases in the city's northwest. A military official said most of the drones were intercepted.
The army-aligned government has since launched a wide-ranging reconstruction campaign and is moving officials back from the Red Sea city of Port Sudan, where they had relocated during the conflict.
More than one million people have returned to the capital within the last ten months, according to the UN's migration agency.
Large parts of Khartoum, however, remain in ruins, with millions still experiencing frequent blackouts linked to RSF drone activity.
The most intense violence meanwhile is now concentrated in the west, where RSF forces have surrounded El-Fasher, the last major city in Darfur not under their control.
The paramilitary force has tried to seize the city for over 18 months.
The UN warned on Monday of escalating violence in North and West Darfur states, with drone strikes and ground clashes reported across both regions.
Despite repeated international efforts to broker a ceasefire, both sides have shown little willingness to compromise.
"We do not want any mercenary or militia to have a role in Sudan's future," Burhan said on Tuesday, referring to the RSF.
The war in Sudan has killed tens of thousands, displaced nearly 12 million and created the world's largest displacement and hunger crises.
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