Background and ObjectivesIn South Africa, the prevalence of human papillomavirus (HPV) and associated diseases, such as cervical cancer and genital warts, is among the highest in the world. This study evaluates the cost-effectiveness of bivalent, quadrivalent, and nonavalent HPV vaccination for 9-to 14-year-old girls from the South African healthcare system perspective. Methods A Markov model portraying the natural HPV disease progression from high-risk infection to cervical intraepithelial neoplasia (CIN) I, CIN II/III, or cervical cancer and from low-risk infection to genital warts was built. Transition probability, utility, and efficacy data were sourced from peer-reviewed literature. Vaccination costs were calculated based on the World Health Organization (WHO) guidelines. The model was populated with a cohort of 520,000 9-year-old girls to calculate incremental cost-effectiveness ratios (ICER) in South African Rand (R) per quality-adjusted life-years (QALYs) gained for each vaccination strategy. Results All HPV vaccination strategies dominate the no vaccine strategy. Compared with the bivalent vaccine, the nonavalent strategy increases QALYs by 0.14 and costs by R1793 (ICER: R13,013 per QALY) per person, while the quadrivalent vaccination provides −0.02 incremental QALYs and R1748 costs (ICER: −R116,397 per QALY). Consequently, at the South African willingness-to-pay threshold of R23,630 per QALY, nonavalent vaccination is the preferred strategy, with a Julia Caroline Michaeli and Thomas Michaeli contributed equally to this work.