The brothers fled to Uganda on the back of a car after seeing their father's body on a street in their village. After arriving in Uganda they were taken to a reception center run by the U.N. refugee agency.
Efforts to support the children have been hurt by a recent scandal in Uganda in which officials were accused of inflating refugee numbers to siphon off aid money. That has shaken international donors.
Aid workers say resources are stretched thin as they try to place the unaccompanied children with foster families with close ethnic ties.
It's crucial to place children with families that speak the same language, said James Kamira, a child protection expert with the World Vision aid agency.
One young mother of two, Beatrice Tumalu, now takes care of eight other children who are not her own.
"I feel pity for them," she said, as she grew up under similar circumstances during the years that South Sudan fought for independence from Sudan. That independence was won in 2011, and South Sudan's civil war broke out two years later.
The unaccompanied children have little of that aid workers call psychosocial support to help deal with trauma. In one refugee settlement just six case workers are available for 78,000 children, according to the Danish Refugee Council.
Another 16-year-old said his parents died three years ago in South Sudan. He walked into Uganda last year and later was placed with a foster family from another ethnic group.
"Staying there, it is not very well," he said of the cultural and communication issues.
Sitting against a tree, he opened the Bible he carried with him and began to cry as he read one passage: "I will not leave you as orphans; I will come to you."
South Sudan's many unaccompanied children need stability and education or "we can lose actually that generation," warned Basil Droti, who is in charge of child protection at one settlement for the Danish Refugee Council.
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