The secondary school systems in Uganda face challenges related to resource allocation, student performance, and cost-effectiveness across different regions. A Bayesian hierarchical model was utilised to analyse data from multiple secondary school systems. The model accounts for heterogeneity among regions and incorporates prior knowledge on resource allocation impacts on student outcomes. The analysis revealed significant disparities in cost-effectiveness across different regions, with a notable 20% variation in per-student expenditure yielding an average of $15 increase in student performance scores. This study provides insights into the optimal resource allocation for secondary schools in Uganda and highlights the importance of considering regional-specific factors to enhance educational outcomes. Policymakers should prioritise investment strategies that reflect these cost-effectiveness patterns, particularly focusing on regions with lower performance scores relative to their expenditure levels. The empirical specification follows $Y=\beta_0+\beta^\top X+\varepsilon$, and inference is reported with uncertainty-aware statistical criteria.