UNICEF and the World Health Organisation (WHO) together with the Sudanese health ministry said in a joint statement that immunisations will begin across Sudan from October 23 to 25, with another wave in November.
Last month, WHO confirmed a case of polio in a two-year-old boy from the violence-stricken region of Darfur, who was found paralysed by the disease.
"The virus has been genetically linked to the virus circulating in (neighbouring) Chad, where six cases were confirmed this year," the joint statement said.
Attacks against humanitarian workers are frequent in Darfur where a four-year civil war has killed at least 200,000 people and displaced two million others.
Khartoum contests the figure and says only 9,000 died in the conflict.
UNICEF representative in Sudan Ted Chaiban urged all parties in the conflict in Darfur to ensure that children are fully protected.
He called for a "firm commitment from those involved in the ongoing conflict in Darfur to guarantee safe access and movement for vaccination teams."
Sudan, which was declared polio-free two years ago, was one of eight African countries to agree in 2005 to carry out mass immunisations against polio, amid a resurgence of the disease despite UN efforts to eradicate it by 2000.