The Rapid Support Forces (RSF) "attacked the village of Um Adam" 150 kilometers (93 miles) south of the city on Saturday, said a statement from the local resistance committee, one of many pro-democracy groups that coordinate aid.
Sudan's war between the military, under army chief Abdel Fattah al-Burhan, and the RSF, commanded by his former deputy Mohamed Hamdan Dagalo, began last April 15.
Many thousands of people have been killed, including up to 15,000 in a single town in the war-ravaged Darfur region, according to United Nations experts.
The war has also displaced more than 8.5 million people, practically destroyed Sudan's already fragile infrastructure and pushed the country to the brink of famine.
Saturday's attack resulted in "over 200 wounded with both serious and minor injuries, and more than 20 martyrs," the statement said.
Five of the wounded succumbed to their injuries, bringing the death toll to 25, the committee said later on Sunday.
A medical source at the Manaqil hospital, 80 kilometers away, confirmed to AFP that they had "received 200 wounded, some of whom arrived too late".
"We're facing a shortage of blood and we don't have enough medical personnel," he added.
More than 70% of Sudan's health facilities are out of service, according to the UN, while those remaining receive many times their capacity and have meagre resources.
Both sides in the conflict have been accused of war crimes, including targeting civilians, indiscriminate shelling of residential areas and looting and obstructing aid.
Since taking over Al-Jazira state just south of Khartoum in December, the RSF has laid siege to and attacked entire villages such as Um Adam.
By March, at least 108 villages and settlements across the country had been set on fire and "partially or completely destroyed", the UK-based Centre for Information Resilience has found.