The attack was one of the deadliest of the clashes in urban areas of Khartoum and elsewhere in Sudan between the military and a powerful paramilitary group known as the Rapid Support Forces.
There was no immediate comment on Saturday from either side of the conflict on the strike and it was not clear whether the attack was by warplanes or a drone.
The military's aircraft have repeatedly targeted RSF troops and the RSF has reportedly used drones and anti-aircraft weapons against the military.
The fighting broke out in mid-April, capping months of increasing tensions between the leaders of the military and the RSF.
Saturday's strike hit the Yormouk neighbourhood in southern Khartoum, where clashes have centred in recent weeks, according to Sudan's Ministry of Health.
The area houses a military facility controlled by the army.
At least 25 houses were destroyed, the ministry wrote in a Facebook post.
The ministry added the dead included five children and an unknown number of women and elderly people, and some wounded people were hospitalised.
A local group that calls itself The Emergency Room and helps organise humanitarian aid in the area said at least 11 people were wounded in the strike.
It posted images it said were of houses damaged in the attack and people searching through rubble.
Other images claimed to show a wounded girl and man.
The conflict has plunged the African country into chaos and turned Khartoum and other urban areas into battlefields.
The paramilitary force has occupied people's houses and other civilian properties since the onset of the conflict, according to residents and activists.
The clashes have killed hundreds of civilians and wounded thousands of others.
More than 2.2 million people have fled their homes to safer areas inside Sudan or crossed into neighbouring countries.
Activists and residents have reported widespread looting in the capital.
Diplomatic missions, including residences belong to the US embassy in Khartoum, have been stormed and looted, allegedly by armed men wearing RSF uniforms.
Almost all diplomatic missions in Sudan were evacuated in the first weeks of the war.
"Looting was fairly extensive at some of the residences," the US Department of State told the Associated Press.
"The damage was discovered during routine checks of the residences. There is some damage to the structures and personal property."
Sexual violence, including the rape of women and girls, has been reported in Khartoum and the western Darfur region, which have hosted some of the worst fighting in the conflict.
The Darfur city of Genena has experienced some of the worst battles, with tens of thousands of its residents fleeing to neighbouring Chad.
The RSF and allied Arab militias have repeatedly attacked the city, especially areas of the non-Arab Masalit community, since late April according to residents and activists.
The attacks intensified earlier this month.
Volker Perthes, the United Nations envoy in Sudan, said last week that the fighting in Genena has taken on "an ethnic dimension" with Arab militias and armed men in RSF uniforms showing "an emerging pattern of large-scale targeted attacks against civilians based on their ethnic identities".
On Wednesday, West Darfur governor Khamis Abdalla Abkar, who hails from the Masalit, was abducted and killed hours after he accused the RSF and allied Arab militias in a televised interview of attacking Genena.
His slaying was blamed on the RSF, a charge the paramilitary force denied.
