As Abdel Fattah al-Burhan departed, medics and witnesses said 39 civilians were killed, most of them women and children, in shelling of Nyala, Sudan's second city in South Darfur state where fighting between the army and paramilitary forces has intensified.
The general was to hold talks with Egyptian President Abdel Fattah al-Sisi, a key ally, on the developments in his country and bilateral ties, said the Sovereign Council, Sudan's highest authority.
Burhan, who traded his trademark military fatigues and green beret for a suit and tie, was greeted by Sisi in Egypt's northern coastal city of El Alamein after flying from Port Sudan, Egyptian media reported.
The conflict between Burhan and his former deputy turned rival Mohamed Hamdan Daglo, who commands the paramilitary Rapid Support Forces (RSF), has raged since April 15.
It has spread from Khartoum and the western region of Darfur to Kordofan and Jazira state, killing thousands and forcing millions to flee their homes.
For months, the RSF had besieged Burhan inside military headquarters in Khartoum, but last week the general made his first public foray outside the compound to review troops in parts of the country.
On Monday, he was in Port Sudan where he made a fiery address to troops, vowing to fight the RSF who he branded mercenaries to "end the rebellion."
"We are mobilizing everywhere to defeat this rebellion, defeat this treason, by these mercenaries who come from all over the world," Burhan told cheering soldiers.
"There is no time for discussion now. We are concentrating all our efforts on the war, to put an end to the rebellion," he said.
His comments came a day after Daglo released a statement detailing a 10-point "vision" to end the conflict and build "a new state."
The plan calls for "civilian rule based on democratic norms" and "a single, professional, national military institution" — the very sticking point which turned the former allies into rivals.
New Darfur violence
Fighting in Nyala on Tuesday killed at least 39 civilians when shelling hit their homes, witnesses and a medical source said.
"The entire members of five families were killed in a single day," said Gouja Ahmed, a human rights activist originally from Nyala.
Images posted online showed dozens of bodies on the ground covered in shrouds as well as men placing the dead in a large grave.
Darfur has long been the site of deadly clashes since a war that erupted in 2003 and saw the feared Janjaweed — precursors of the RSF — unleashed on ethnic minority rebels.
Since August 11 more than 50,000 people have fled Nyala due to the violence, the United Nations says.
There was also violence in Khartoum where late Monday the army bombarded several RSF positions, according to residents.
Port Sudan, which has been spared the violence tearing apart Sudan, is where government officials and the U.N. have relocated operations. It is also the site of Sudan's only functioning airport.
Before they fell out, Burhan, backed by Daglo, became Sudan's de facto ruler in a 2021 coup that derailed a fragile transition to civilian rule.
The coup upended a transition painstakingly negotiated between military and civilian leaders following the 2019 ouster of longtime autocrat Omar al-Bashir.
Burhan's latest trip follows multiple diplomatic efforts to broker an end to the violence in Sudan, with a series of U.S.- and Saudi-brokered ceasefires being systematically violated.
In July, Egypt, which shares borders with Sudan and has been flooded by refugees from its neighbor, hosted a crisis meeting attended by African leaders to seek a solution.
Conservative estimates from the Armed Conflict Location & Event Data project show that nearly 5,000 people have been killed in the conflict.
But the real figure is thought to be much higher, and the U.N. says more than 4.6 million people have been displaced by the fighting both inside and outside Sudan.