The survey published in BioMed Central's International Journal for Equity in Health showed that boys were most often assaulted by adult women, followed closely by other schoolchildren.
"This study uncovers endemic sexual abuse of male children that was suspected but hitherto only poorly documented," Neil Andersson and Ari Ho-Foster of the Centre for Tropical Disease Research in Johannesburg wrote.
The findings underscore the need to raise awareness about the rape of male children and they urged further efforts to prevent sexual violence in South Africa, the researchers said.
Another problem is that the prevalence of rape is hampering efforts to combat AIDS in a country at the epicentre of the global pandemic.
"There is increasing recognition of links between sexual abuse and high-risk attitudes to sexual violence and HIV risk," the researchers wrote. "Sexually abused children are also more likely to engage in HIV high-risk behaviour."
The survey carried out in 1,200 schools across the country asked 127,000 boys aged between 10 and 19 if they had ever been sexually abused and, if so, by whom.
Abuse by fellow males was more common in rural areas while attacks by women happened mainly in cities, the study found.