The school, funded by philanthropists, offers hope to children who would typically get left behind in a country still plagued by inequality decades after the end of apartheid.
"Most of them, unfortunately, don't have a nice background, mostly the parents don't work," said Lebogang Gobodo, 25, a former student who is now employed by the Ubuntu Pathways project.
"So, with us what's different is that we then tend to give them food packages at the end of the month. They also attend a clinic here. So we try to cover everything," she said.
Jacob Lief, a co-founder of Ubuntu Pathways, said the idea is to invest "in disadvantaged children the same way we're investing in privileged children."
Among the 2,000 children who have been through the center over the past 25 years of its existence, most were born to HIV-positive mothers.
The center houses a clinic which specializes in caring for pregnant women with HIV/AIDS, 600 of whom are currently receiving free treatment.
"One of the keys to keeping a young child healthy and going through school and eventually matriculating is keeping the mother healthy and alive," said Lief.
All the babies delivered over the past here have been born free of HIV.
Most of the children go on to study at the center's school.
Along with funding by philanthropists, the school's $7 million annual budget is also funded by local companies.
The modern concrete structure stands cheek-by-jowl with rows of modest brick houses and corrugated iron structures in an impoverished area with thousands of inhabitants in the coastal city of Gqeberha.
Many in the neighborhood did not complete school and most households live off a small government social welfare.
If the Ubuntu Pathways project did not exist "these kids may not be at school at all," said a 32-year-old teacher, Taneal Padayachie.
Decades after the end of white rule, the effects of a two-tier apartheid system which offered inferior education to Black South Africans, are still being felt.
Eight out of 10 schoolchildren aged nine or ten struggle to understand what they read, according to a study published last month.
46-year-old Lief, originally from New York, arrived in South Africa at age 17.
After completing college, he returned to South Africa, where a meeting with local teacher Malizole "Banks" Gwaxula led to a six-month stay in which the two worked on community projects.
The two then set up their NGO, based on the essence of humanity that South Africans simply call 'Ubuntu,' meaning "I am because you are."
The idea was also to offer something different from other charities that come "distribute soccer balls" to children in townships, "take photos" and return overseas.
Children's "birthplace shouldn't have to determine their future", said Lief.