While multiple studies have documented shifting educational gradients in HIV prevalence, less attention has been given to the effect of school participation and academic skills on infection during adolescence. Using the Malawi Schooling and Adolescent Study, a longitudinal survey that followed 2,649 young people aged 14–17 at baseline from 2007 to 2013, we estimate the effect of three education variables: school enrolment, grade attainment, and academic skills—numeracy and Chichewa literacy—on herpes simplex virus type 2 (HSV-2) and HIV incidence using interval-censored survival analysis. We find that grade attainment is significantly associated with lower rates of both HSV-2 and HIV among girls, and is negatively associated with HSV-2 but not HIV among boys. School enrolment and academic skills are not significantly associated with sexually transmitted infections (STIs) for boys or girls in our final models. Efforts to encourage school progression in high-prevalence settings in sub-Saharan Africa could well reduce, or at least postpone, acquisition of STIs.