Studies have shown that school-based sexual health promotion interventions can improve adolescent sexual and reproductive health outcomes. However, there has been insufficient evidence on the cost and cost-effectiveness of such programmes, driving poor and inconsistent investment and prioritization. This paper analyses the costs of the SKILLZ Health for Girls programme, a sports-based sexual education intervention targeted at adolescent girls in the secondary school environment. Costs were collected alongside a cluster-randomized trial, including 38 secondary schools in Cape Town, South Africa. The analysis was conducted from a provider (multi-sector) perspective and used a mixed-method costing approach. We developed a cost data collection tool to compile cost information from one-on-one interviews, administrative data, and non-participant observations of the intervention. Costs were analysed for 2019, representing a full academic year of programme implementation. The intention-to-treat analysis revealed an average cost per learner per session of $9.92, and the cost per learner reached was estimated at $69.43. Sensitivity analysis indicated that these costs were sensitive to the participation rates of the learners who did not complete the intervention. The cumulative cost for the scale-up scenario for the Western Cape province based on the base-case analysis (maximizing coverage of schools but only including 30$ of eligible learners within schools) was estimated at $5 311 453.00 for a 3 year period which exceeds the provincial conditional grant allocation dedicated to the HIV and AIDS (Life skills education) for the same period, yet is comparable to the expenditure for a similar donor-funded programme within the province. The study’s results will contribute to decision-making for implementing sexual education interventions in schools in South Africa and similar contexts.