Juba, Khartoum and the United nations agreed in July to send food aid to South Sudan, where fighting flared last month in the country's 11-month civil war.
The first 18 trucks crossed into South Sudan on Saturday, "carrying some 700 metric tons of food for 45,000 people for one month", UN Resident Coordinator and Humanitarian Coordinator in Khartoum Ali Zaatari said in an announcement.
It was also signed by Sudan's Humanitarian Aid Commission, the South Sudanese embassy in Khartoum and the World Food Programme.
A political dispute between South Sudanese President Salva Kiir and his former deputy Riek Machar has degenerated into a brutal ethnic conflict between their Dinka and Nuer peoples, driving 1.8 million people from their homes.
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Fighting erupted again in October at the end of the rainy season, which makes many roads in the country impassable.
Hundreds of thousands of people have fled across the border to camps in Sudan.
Juba split from Sudan in 2011 under a peace agreement that ended a bloody 22-year civil war in the formerly united country.