These children, who sleep on the steps of buildings or in abandoned market stalls, are the fallout of the 21-year civil war that split their region apart; many of them can barely remember the families they were torn from by the violence that engulfed their villages, forcing them to run.
Nobody knows exactly how many children are living on Juba's streets, and few non-governmental organisations (NGOs) are working with them; there is no social service in place to help them locate their families or assist with family reintegration.
Relief workers in the area say that with little or no family support, no education and no protection, street children are increasingly at risk of sexual abuse and HIV.
James Mabior*, 15, is wiry and small for his age. He told IRIN/PlusNews that his family had fled the fighting in their village, but his mother had died shortly after arriving in Juba and his father was an alcoholic.
"My father was beating me at home - whenever I did a mistake he beat me. He told me that he was sick with malaria and he left to go back to our village," he said. "After that there was nobody to care for me so I came to the market." He had been living on the streets for at least three years.
Like the other boys he lives with in Konya Konya Market, Mabior survives by begging and scavenging food from local restaurants. He does not go to school and has no access to even the most basic of healthcare facilities.
One of the main dangers faced by homeless boys and girls is the sexual predators. "Sometimes it happens that men come and look for boys for sex; they are looking for boys and girls, but where I stay there are only boys," Mabior said.
"It is a mixture: Arabs, southerners, soldiers from all over ... some boys will go straight away for the money, others will resist and refuse, but this means they can get beaten." He said the children earned between US$0.05 and $0.10 for providing sexual services.
Although Mabior had heard of HIV, he had no real understanding of how it is spread, or the dangers posed by unprotected sex.
"I can get it [HIV] from eating rotten food; this is the only way I know that you catch it," he said. "Nobody in my family ever informed me about this thing ... I left school a long time ago and am willing to go back, but I can't because I have no money."
Ben Poggo*, who lives in Juba's Crown Market, said, "I have heard of HIV; if you have it you will slim up. AIDS comes through dirty things - you must keep clean and wash so that you don't get it, but for us to keep clean on the streets is hard."
Mary Isaac runs the Living Water Children's Home, a centre for 37 boys who used to live on the streets. "Boys living on the streets have no protection and are vulnerable to sexual abuse by many people," she said.
"There is only one NGO doing educational work with these children in a very limited capacity, and the numbers of children are growing daily. Many are too scared to seek out help, and will not talk about the abuse they suffer."
Rev Benjamin Lokio Lemi, head counsellor at Juba's voluntary counselling and HIV testing centre, told IRIN/PlusNews that street children were particularly vulnerable to HIV because they lacked knowledge about transmission and few knew their status or went for treatment.
"There needs to be a campaign to raise awareness of HIV amongst children living on the streets; children need to be encouraged to know their status so they can avoid risky behaviour," Lemi said. "But testing is voluntary, and they will only come forward to be tested if they have been educated."
The government of South Sudan is developing legislation that will put in place systems for the care and protection of vulnerable children, including street children, and police in the region have received some training on child protection.
*Names have been changed