General Abdel Fattah al Burhan also renewed his commitment of withdrawing the military from politics in Sudan at a peace forum in Ethiopia.
Demonstrators marched across Sudanese cities to mark the deadly sit-in protests during the military takeover of the government where over 60 people were killed in the capital Khartoum in 2019.
At least seven people were killed after security forces used gunfire and tear gas to disperse demonstrations against last year's military coup.
The United Nations has said it will hold talks in Sudan aimed at salvaging a fragile democratic transition amid a grinding stalemate following an October coup.
Hamdok’s deal with the coup leaders did not stop protests, leading to his resignation, giving way to greater uncertainty.
Prime Minister Abdalla Hamdok's resignation comes as thousands rally against the military in the northeastern African country.
Khartoum residents continued to protest Sudan’s military rule in the streets after security forces cracked down the rally that left several people dead.
From Gulf countries lifting the Qatar blockade to the bombing of Gaza and a coup in Sudan, these were some of the moments that shaped the Middle East.
Troops deployed across Sudan's Khartoum and closed almost all bridges over the Nile River linking the capital with its twin city of Omdurman and the district of Bahri.
Prime Minister Abdalla Hamdok tells a group of political and intellectual figures that he will step down, Reuters news agency reports, citing sources close to Hamdok.
Several demonstrators were injured after police fired tear gas canisters at activists near the presidential palace in Khartoum.
Civilian groups reject political deal between army chief and prime minister, calling for continuing protests against military rule.
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