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21st century

The sudden death of SPLA head and vice-president of Sudan John Garang in late July 2005, was followed by three days of violent riots in the capital. Order was finally restored after southern Sudanese politicians and tribal leaders sent strong messages to the rioters. The death toll was at least 24, as youths from southern Sudan attacked northern Sudanese and clashed with security forces.

The African Union summit of 16–24 January 2006 was held in Khartoum; as was the Arab League summit of 28–29 March 2006, during which they elected Sudan the Arab League presidency.

On 10 May 2008, the Darfur rebel group Justice and Equality Movement attacked the city with the goal of toppling Omar al-Bashir 's government. The Sudanese government held off the assault.

On 23 October 2012, an explosion at the Yarmouk munitions factory killed two people and injured another person. The Sudanese government claimed that the explosion was the result of an Israeli airstrike.

On 3 June 2019, Khartoum was the site of the Khartoum massacre, where over 100 dissidents were murdered (the government said 61 were killed), hundreds more injured and 70 women raped by Rapid Support Forces (RSF) soldiers in order to forcefully disperse the peaceful protests calling for a civilian government.

On 1 July 2020, activists demanded that al-Zibar Basha street in Khartoum be renamed. Al-Zubayr Rahma Mansur was a slave trader and the al-Zibar Basha street leads to the military base where the 2019 Khartoum massacre took place.

On 26 October 2021, the city was locked down following a military coup that left at least 7 dead, triggering protests and calls for a general strike. Prime minister Abdalla Hamdok was arrested during the coup, and held along with other cabinet members in an unknown location.

On 15 April 2023, fighting between the Sudanese Armed Forces and the RSF broke out across Sudan, including in Khartoum. Fighting was reported at the presidential palace, the RSF's headquarters, Khartoum International Airport and Merowe Airport, the last two of which the RSF claimed to have captured. Gunfire and clashes were also reported at El Obeid Airport in North Kordofan.