Objective To characterise perceived household support for female education and the associations between educational support and HIV prevalence, HSV-2 prevalence and sexual risk behaviours. Methods This cross-sectional study used baseline survey data from the Swa Koteka HPTN 068 trial undertaken in Mpumalanga, South Africa. The study included 2533 young women aged 13–20, in grades 8–11 at baseline. HIV and HSV-2 status were determined at baseline. Information about patterns of sexual behaviour and household support for education was collected during the baseline survey. Linear regression and binary logistic regression were used to determine associations between household support for education and both biological and behavioural outcomes. Results High levels of educational support were reported across all measures. HIV prevalence was 3.2% and HSV-2 prevalence was 4.7%, both increasing significantly with age. Over a quarter (26.6%) of young women reported vaginal sex, with 60% reporting condom use at last sex. The median age of sexual debut was 16 years. Household educational support was not significantly associated with HIV or HSV-2; however, the odds of having had vaginal sex were significantly lower in those who reported greater homework supervision (OR 0.82, 95%CI: 0.72–0.94), those who engaged in regular discussion of school marks with a caregiver (OR 0.82, 95%CI: 0.71–0.95) and when caregivers had greater educational goals for the young woman (OR 0.82, 95%CI: 0.71–0.96). In contrast, greater caregiver disappointment at dropout was significantly associated with reported vaginal sex (OR 1.29, 95%CI: 1.14–1.46). Conclusion Young women in rural South Africa report experiencing high levels of household educational support. This study suggests that greater household educational support is associated with lower odds of having vaginal sex and engaging in risky sexual behaviour, though not with HIV or HSV-2 prevalence.