Background: Intervention effects observed in efficacy trials are rarely replicated when the interventions are broadly disseminated, underscoring the need for more information about factors influencing real-life implementation and program impact. The ongoing national implementation of an evidence-based HIV prevention program in The Bahamas permits examination of implementation patterns over time and their relationship to long-term student outcomes. Methods: Data were collected from national implementation between 2011-2014, involving 208 grade 6 teachers, 75 grade 7 teachers, 58 grade 8 teachers and 4,411 students initially in grade 6 and followed for three years. Structural equation modeling and mixed-effect modeling analyses were applied. Results: Teachers' attitudes towards and comfort with the intervention curriculum, and attendance at the curriculum training workshop had a direct effect on teachers' patterns of implementation, which had a direct effect on student outcomes. Teachers' attitudes had a direct positive effect on student outcomes. Teachers' training in interactive teaching and longer duration as teachers were positively associated with teachers' confidence in teaching the curriculum. High quality implementation in grade 6 was significantly related to student outcomes in grades 6 and 7 post-implementation. Level of implementation of the booster sessions in grades 7 and 8 were likewise significantly related to subsequent student outcomes in both grades. Conclusions: High quality initial implementation of a prevention program is significantly related to better program outcomes. Poor subsequent delivery of booster sessions can undermine the positive effects from the initial implementation while strong subsequent delivery of booster sessions can partially overcome poor initial implementation.