The International Committee of the Red Cross said the children were evacuated from an orphanage in Khartoum, where they were trapped by ongoing fighting.
Aid agencies have managed to rescue more than 280 infants, toddlers and older children, along with 70 caregivers from an orphanage that has found itself in the midst of heavy fighting in Sudan's capital, Khartoum.
The evacuation comes after more than 70 children died from hunger and illness in the facility since mid-April.
The International Committee of the Red Cross (ICRC) said on Thursday that one of its teams had managed to facilitate the evacuation of the Maygoma Orphanage.
"Knowing these children are safe is an enormous relief," Jean-Christophe Sandoz, the head of the ICRC delegation in Sudan, said.
According to the ICRC said the children were aged between 1 month and 15 years and some were suffering from mental health conditions which the agency said could be worsened by the extremely stressful conditions they were having to endure.
"They spent incredibly difficult moments in an area where the conflict has been raging for the past 6 weeks without access to proper healthcare, an especially hard situation for children with special needs," the ICRC said in a statement.
Fighting between Sudan's army and the paramilitary Rapid Support Forces (RSF) near the facility meant that only some of the staff were able to care for the hundreds of children.
With not enough care, food or hydration, children began to die in the state-run facility as fighting raged nearby.
The aid organization said it managed to secure security guarantees from the warring parties to allow safe passage for the children and orphanage staff, who have been taken to Wad Madani, situated around 200 kilometres from Khartoum.
According to the UN children's agency UNICEF, the situation for children in the country is worsening as each day of fighting passes. UNICEF estimates that around 13.6 million children are dependent on humanitarian aid.
The fighting, ongoing since mid-April, has killed hundreds and displaced over a million people, hundreds of thousands of whom have crossed into neighbouring countries to seek refuge.