More than 8,000 children are still missing as tracers confront rough terrain.
A South Sudan family of seven was reunited after five years on Tuesday under the Family Tracing and Reunification programme.
Save the Children, the agency that runs the programme, said this brings to 6,000 the number of children reunited with their families since 2014 following separation by war.
However, more than 8,000 children in the country are still missing as long distances and poor connections make the tracing by case workers quite labour intensive.
Child number 6,000, Nyandor, 17, together with her four sisters and brothers was reunited with the parents in Bentiu on April 16, 2019.
They had been separated from their parents during an attack in Bor in 2014 as the family scampered in different directions for safety.
“It was an emotional moment for everyone involved. “It was ululation, tears, and songs of happiness,” said Arshad Malik, Interim Country Director for Save the Children International South Sudan.
"Seeing the happiness in their faces after enduring so much fills us with hope. We won’t stop until all separated children are back home,” Mr Malik said.
More than four million people have been displaced by the war with unaccompanied children being more susceptible to violence, abuse and exploitation.
The peace agreement signed in September 2018 has seen more refugees return to South Sudan from neighboring countries.
The ceasefire has also given access to areas that were previously inaccessible, making tracing easier.
“Despite all the difficulties, almost every week we see one or several children brought back to their families.
“To bring the rest of the children back home, we need strong partnerships and support from the international community,” said UNICEF representative in South Sudan Mohamed Ag Ayoya.