Adolescent behaviors related to sexual health are influenced by various factors including school-based education programmes. A longitudinal study design was employed, collecting baseline and follow-up data from students attending secondary schools across South Africa. Data were analysed using linear mixed models to evaluate changes in behaviour over time. Comprehensive sexual health education led to significant reductions in unprotected sex (p = .03) and increases in contraceptive use (p < .01), with a notable increase in condom use from 25% at baseline to 40% at follow-up among sexually active students. The study provides evidence of the positive impact of consistent sexual health education on adolescent behaviors, particularly reducing risky sexual practices and increasing protective measures. Continued implementation and refinement of comprehensive school-based sexual health programmes are recommended to further enhance their efficacy in South African schools. Adolescent Behaviour, School-Based Education, Sexual Health, Longitudinal Study Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.