Officials said seven million people in the African country are facing a hunger crisis as the lean season between harvests approaches and fighting continues.
The Scottish-based charity, which provides a daily meal to children attending school in some of the poorest parts of the world, has worked in South Sudan since 2008.
It already feeds more than 20,000 children but more young people are now trying to enrol at schools serving Mary's Meals as a number of other schools have been destroyed in the war.
Charity founder and chief executive Magnus MacFarlane-Barrow said: "The plight of children in South Sudan is truly heartbreaking.
"For them, the promise of a daily school meal has never been more important.
"We are determined to keep our promise to the 1,257,278 children around the world who rely on Mary's Meals.
"With more hungry children arriving at schools in South Sudan each day, we also need help to meet the growing demand there.
"We hope to ensure that every new child enrolling at schools in South Sudan already serving Mary's Meals can receive a daily meal and, as funds allow, also expand our programme to reach 1,657 additional children at five new schools there.
"We can do this with support while continuing to expand our programme around the world to reach many more children."
Mary's Meals has been working with the Diocese of Rumbek to feed children at 40 schools in the area.
Education co-ordinator Moses Kopurot Kenyi said: "It's a terrible situation. Many of the children are displaced or without their parents. They are very traumatised.
"There is a lot of hunger and people are just eating leaves from trees. Mary's Meals' feeding programme is helping us a lot. For these children, there is no other source of food.
"Education is really important for helping to build peace. Without education, the situation will never change and the division and anger will still be there."
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