The evaluation of secondary school systems in Uganda is critical for understanding their effectiveness and identifying areas for improvement. Current methods often lack a robust theoretical framework to guide cost-effectiveness assessments. The proposed framework integrates statistical modelling and experimental design principles. A cost-utility analysis will be conducted using logistic regression models with robust standard errors to estimate the impact of interventions on student outcomes. The developed methodological approach provides a robust tool for policymakers and educators to evaluate the efficacy of educational interventions in Uganda and beyond. Policymakers should prioritise research-based evidence when designing and implementing educational reforms. Theoretical frameworks like this one can serve as a foundation for future empirical studies. The empirical specification follows $Y=\beta_0+\beta^\top X+\varepsilon$, and inference is reported with uncertainty-aware statistical criteria.