South Sudan, one of the world's poorest countries, has more than 150,000 refugees from Sudan. Both sides reached the brink of war this year amid disputes over unsettled border regions.
WFP said it was dropping more than 2,000 tons of food in parts of the country by air because of the lack of infrastructure needed to deliver humanitarian assistance.
"WFP is pulling out all the stops to keep providing desperately needed food to refugees in Upper Nile state," Chris Nikoi, WFP country director, said in a statement.
U.S. Secretary of State Hillary Clinton arrived this week in South Sudan to meet with leaders in Juba. She's the highest-ranking U.S. official to visit the country since it gained independence from Sudan in 2011.
South Sudan's independence was secured under the terms of a comprehensive peace agreement reached with Washington's help in 2005.
A deadline imposed by the United Nations for both sides to settle outstanding issues left from the 2005 agreement expired Thursday.