The 311 children, including 87 girls, will now begin reintegrating into their communities, the UN mission in the country (UNMISS) said in a statement on Wednesday.
"Children should not be carrying guns and killing each other," said David Shearer, head of UNMISS.
"They should be playing, learning, having fun with friends, protected and cherished by the adults around them."
The children's release was marked at a ceremony in the city of Yambio.
Shearer said this was the first time that "so many young women" had been involved in a release like this in the war-torn country.
"They will have endured suffering, including sexual abuse. It is vital that they receive the support they need to rejoin their communities and that they are welcomed home by family and friends without any sense of stigma."
According to the UN mission's research, the South Sudan Liberation Movement had recruited 563 children, while some 137 were associated with the Sudan People's Liberation Army In-Opposition.
South Sudan was founded with optimistic celebrations in the capital on July 9, 2011, after it gained independence from Sudan in a referendum that passed with close to 100 percent of the vote.
But the country descended into conflict in December 2013 after President Salva Kiir accused Riek Machar, his former deputy who he had sacked earlier that year, of plotting a coup, prompting a civil war.
According to UNICEF, the UN's children agency, both sides are using children to fight.
Multiple attempts at peace deals have failed. A peace accord was signed in August 2015, however, the deal fell apart and fighting continued.
The war has resulted in tens of thousands of people being killed and a quarter of the country's 12 million population forced from their homes.
According to the UN, six million people - half of the country's population - are in desperate need of humanitarian assistance, while more than 1.2 million are at risk of famine.