The 6,000-mark was reached on Thursday with the reunification of five siblings with their parents in Bentiu (former unity state).
They had been separated during an armed attack in Bor in 2014 when they were scattered by the violence.
In a statement, Interim Country Director for Save the Children International South Sudan Arshad Malik said the reunification was an emotional moment.
He said: “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.”
According to the statement, there are more than 8,000 children still missing or are separated and in urgent need of family tracing.
“Separated and unaccompanied children are more susceptible to violence, abuse and exploitation, which makes returning them to their parents an urgent priority for UNICEF, Save the Children and partners,” the statement partly read.
The UNICEF representative in South Sudan Mohamed Ag Ayoya called on the international community and urged strong partnerships in the process of tracing and reunification which is labor intensive.
“Despite all the difficulties, almost every week we see one or several children brought back to where they belong, namely with their families. This is much thanks to all family tracing and reunification partners in South Sudan,” he said.
With adequate funding, implementation of the September peace deal which will allow access to areas previously inaccessible, the organizations say the tracing and reunification programme will be secured.