Around 300,000 unaccompanied and separated children were documented by UNICEF in 2015 and 2016 compared to only 66,000 in 2010 and 2011.
A new report released on Thursday outlines the vulnerability children face as refugees and urges to governments do more to help the growing crisis.
The report outlines how vulnerable unaccompanied children are and highlights an increase in children using people smugglers and traffickers on their journeys.
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First famine declared in six years, in South Sudan
UNICEF deputy executive director, Justin Forsyth, said children were particularly vulnerable to abuse and exploitation by people smuggling syndicates.
"Ruthless smugglers and traffickers are exploiting their vulnerability for personal gain, helping children to cross borders, only to sell them into slavery and forced prostitution,” Mr Forsyth said.
“It is unconscionable that we are not adequately defending children from these predators."
Children make up just under 30 per cent of human trafficking victims around the world, but in Sub-Saharan Africa and Central America, that number is above 60 per cent.
Speaking from the largest refugee camp in the world in Uganda, World Vision chief advocate, Tim Costello, said the organisation has registered thousands of children travelling alone in the last 10 months.
“We have now registered 9000 unaccompanied and separated children, children who don't know whether their parents are alive or dead, who are just told to follow the crowd coming from South Sudan here,” Mr Costello said.
Famine and violence in South Sudan has triggered the largest movement of refugees in Africa since the Rwandan genocide.
Mr Costello describes the situation as “the forgotten crisis for the world”.
“The situation here in Uganda is much more dramatic in it’s rawness, in its poverty and people being on the edge than what I have seen anywhere else,” he said.
Nearly two million people from a population of 12 million have fled South Sudan in the growing crisis - one million of those fleeing are children.
"There is no sadder evidence of the extent of violence and hunger in South Sudan than the sight of children crossing borders without parents or family," Mr Costello said.
"They have been shot at, they have seen their parents killed, they are hungry, they are dressed in rags, and too often they have been abused along the way, it is horrific and heartbreaking."
