Although young people in South Africa are growing up in an era where their socioeconomic circumstances are seemingly better than those of their parents’ generation, they face greater risks in their trajectory to adulthood. This is mainly because the environment in which they are making sexual decisions is also rapidly evolving. Currently, South Africa has the highest prevalence of HIV and AIDS in the world among young people aged 15–24. This study examined the effect of sexual behaviours initiated in adolescence on enrolment in post-secondary education. The analysis was conducted using data from the longitudinal Cape Area Panel Study (CAPS, Waves 1–5) conducted in 2002–2009, which focused on young people’s sexual behaviours in Cape Town, South Africa. The sample was restricted to 3213 individuals who reported sexual debut during adolescence. Using logistic regression models fitted separately for males and females, the results revealed that several factors acted as either hindrances or protective factors to enrolment in post-secondary education. Early sexual debut (by age 17) was negatively associated with participation in tertiary education. Other variables that had a negative effect included not using contraception at first sex, parenthood, engaging in risky behaviours such as illegal substance use, cigarette smoking and drinking alcohol and neglect of school homework (doing less than an hour a day). Higher levels of parental education (except for paternal education in the female model), urban residence and higher aspirations and analogous behaviours (studying) acted as protective factors and were positively associated with post-secondary education initiation. The paper also points to the relationship between early sexual debut and persistent socioeconomic inequality and provides empirical evidence for re-thinking policy development and implementation around schooling and sex education.