The drone attack occurred at the same time hospitals were receiving children for an ongoing vaccination campaign, including the hospital in al-Jabalain in the southeast of the country.
In the civil war in Sudan, the paramilitary Rapid Support Forces (RSF) are fighting the country's army, but the civilian population is hardest hit, with tens of thousands of deaths and millions displaced.
RSF is believed to be behind the attack.
Doctors Without Borders said it was helping to transport patients and injured people to hospitals in a city 80 kilometers away.
The neighboring country of Chad also came under drone attacks on Thursday.
