Egyptian national carrier EgyptAir will run its first direct flight from Cairo to Port Sudan starting on Friday, the Egyptian Civil Aviation Ministry said on Tuesday.
The decision comes after Sudanese authorities reopened airspace in the eastern sector of the country, after closing it entirely after the war broke out on April 15.
Khartoum International Airport has been making exceptions for humanitarian and evacuation flights, subject to the right permits being obtained by relevant authorities.
The war between army chief Gen Abdel Fattah Al Burhan and his former deputy, RSF commander Gen Mohamed Dagalo, has killed at least 3,900 people, according to a conservative estimate, and displaced around 3.5 million.
Sudan's army chief returned home on Tuesday after visiting Egypt on his first trip abroad since the outbreak of the fighting, with the latest violence killing dozens of civilians in battle-scarred Darfur.
As Mr Al Burhan travelled for talks with key ally Egyptian President Abdel Fattah El Sisi, medics and witnesses said 39 civilians were killed, most of them women and children, in the shelling of Nyala, the South Darfur state capital where fighting between the army and paramilitary forces has intensified.
During his brief trip to Egypt, Mr Al Burhan said his forces faced "rebel groups who have committed war crimes in their attempt to seize power".
Western countries have accused the paramilitaries and allied militias of killing based on ethnicity and the International Criminal Court has opened a new inquiry into alleged war crimes.
The army has also been accused of abuse, including a July 8 air strike that killed about two dozen civilians.
Mr El Sisi's office said he had "reaffirmed Egypt's firm position in standing by Sudan and supporting its security, stability and territorial integrity" during the meeting.