This is the second attack where civilians have been killed since the country's military recaptured central Khartum two days ago.
The paramilitary RSF is believed to be behind the attack, according to the Emergency Lawyers Network, which documents abuses by both the military and RSF.
On Sunday, three civilians, including two children, were killed in an artillery attack in Omdurman near the capital.
The military launched an offensive on Friday. Since then, both the central bank's headquarters and the presidential palace have been retaken from RSF, which has controlled the area since the civil war broke out in April 2023.