Background: Women leaders are significantly underrepresented in health policy and programme decision-making globally, and this gap often begins in adolescence. Namibia faces persistently high teenage pregnancy rates; a public health crisis linked to school dropout and constrained economic futures- yet adolescent girls are rarely positioned as future public health leaders or agents of community change. We hypothesised that early preparation of girls as informed decision-makers and civic advocates, integrated with Sexual and Reproductive Health and Rights (SRHR) education, leadership skill development, and body autonomy training, would not only improve health knowledge and agency but also establish foundational competencies for girls to become future women leaders shaping reproductive and public health outcomes in their communities. Methods: A convergent mixed-methods design was applied in a pilot secondary school in Namibia. Baseline and post-intervention assessments measured SRHR knowledge, self-reported decision-making confidence, and emerging leadership competencies. Qualitative data were collected through participatory learning sessions, focus group discussions, and facilitator reflections. A Training-of-Trainers (ToT) model built local capacity among teachers and youth mentors, positioning them as advocates for girls’ leadership development. Learner-led leadership clubs were established to sustain peer education and community advocacy beyond the intervention. Fifty-seven (57) female secondary school learners participated, with teachers and community stakeholders as secondary participants. Results: Post-intervention assessments showed statistically significant improvements in SRHR literacy and self-reported decision-making confidence. Importantly, girls demonstrated emerging leadership competencies: greater capacity to advocate for themselves and peers, initiate health conversations with trusted adults, and envision themselves as agents of community health promotion. Learner-led clubs sustained high engagement, functioning as spaces where girls developed peer advocacy skills. Qualitative data revealed a fundamental shift in self-perception: girls moved from viewing themselves as passive recipients of health information to identifying as advocates for their own and their peers’ reproductive and health rights. Curriculum alignment with the Namibian Ministry of Education framework, along with buy-in from school and community leaders, positioned the programme for policy integration and scale-up. Evidence of programme sustainability was demonstrated through local facilitator capacity-building and the autonomous functioning of learner-led clubs beyond external facilitation. Conclusions: A school-based, multi-component intervention that integrates SRHR education, body autonomy training, and explicit leadership development cultivates girls as informed decision-makers and establishes early pathways to women’s leadership in health. The model demonstrates feasibility, cultural acceptability, and effectiveness in sub-Saharan Africa and addresses a critical gap in women’s pipeline development for public health leadership. Integration into national adolescent health policy and expansion to secondary schools nationally is warranted. The intervention’s embedding of sustainability mechanisms— through a Training-of-Trainer’s approach and learner-led clubs—positions the programme for continuation as standard school health practice. This work contributes to building the evidence base for leadership-informed public health interventions and demonstrates how strengthening girls’ civic participation and community advocacy competencies during secondary school establishes foundations for lifelong engagement in health policy and systems change.