The secondary schools system in Kenya faces challenges related to energy efficiency and cost-effectiveness. A Bayesian hierarchical model was developed to estimate the cost-effectiveness of different energy technologies used in Kenyan secondary schools. The model accounts for variability at multiple levels including school-specific characteristics and regional differences. The analysis revealed that solar photovoltaic systems were most cost-effective, with an estimated average return on investment within a 95% credible interval of [1.2 to 3.4] years. This study provides evidence supporting the adoption of solar energy solutions in secondary schools as a viable and financially beneficial approach. School administrators should prioritise the implementation of cost-effective renewable energy systems, such as solar photovoltaics, based on this model’s findings. The empirical specification follows $Y=\beta_0+\beta^\top X+\varepsilon$, and inference is reported with uncertainty-aware statistical criteria.