The voluntary repatriation of 147 refugees is the first such return by some of the hundreds of thousands of Sudanese who fled the country during its long-running civil war.
"This first group is a hope for the future for all Sudanese refugees and displaced," Tesema Negash, the director of the World Food Program's operations in Kenya, said in a statement.
The U.N. refugee agency was transporting the group from Kenya's Kakuma camp to Sudan's Eastern Equatoria state, said Peter Smerdon, a spokesman for the World Food Program.
About 560,000 Sudanese living in camps and settlements in seven neighboring countries are expected to go home after Sudan's government and the main southern rebel group signed a deal in January to end a 21-year war. An additional 4 million displaced people within Sudan are also likely to return in coming years.
"The problems caused by 21 years of civil war are not going to disappear overnight. Bringing all the Sudanese home will take a long time and needs the international community's support to happen," Negash said.
The repatriations have been delayed because many of the refugees' homes were destroyed in the war. There are few hospitals or schools in southern Sudan, and the region lacks good roads, running water and electricity.
The southern civil war pitted the Arab Muslim-dominated government in Khartoum against rebels fighting for greater autonomy and a larger share of the country's wealth in the largely African animist and Christian south.
More than 2 million people died in the conflict, mainly from war-induced famine and disease.
The north-south peace accord provides for an autonomous south with its own army, government and a new constitution during a six-year interim period. After the transition, the 10 southern states are to hold a referendum on independence