Nigeria's secondary school systems have faced challenges in ensuring cost-effectiveness despite significant investments. The study employs a cost-efficiency analysis with Stata, utilising secondary school expenditure and output data from to . Panel data regression models are applied to assess the impact of various factors on efficiency scores, accounting for within-school heterogeneity. Panel-data estimates reveal that school size has a significant negative effect on cost-efficiency (p < 0.05), suggesting larger schools may struggle with resource allocation and management. The econometric model highlights the importance of addressing inefficiencies in large secondary schools to improve overall system effectiveness. Efforts should focus on providing targeted support to underperforming large schools, such as additional financial assistance or training for school administrators. Model estimation used $\hat{\theta}=argmin_{\theta}\sum_i\ell(y_i,f_\theta(x_i))+\lambda\lVert\theta\rVert_2^2$, with performance evaluated using out-of-sample error.