Community health centres in Nigeria play a crucial role in primary healthcare delivery, but their cost-effectiveness remains underexplored. A multilevel regression model was employed to analyse data from 50 health centres across 10 states, accounting for both individual-level patient characteristics and contextual-level factors such as geographical location and socio-economic status. Robust standard errors were used to account for potential heteroscedasticity. The analysis revealed significant variations in service outcomes among different regions, with a regression coefficient indicating that urban centres had better health indicators compared to rural counterparts (p < 0.05). Community health centres exhibit varying levels of cost-effectiveness across Nigeria, necessitating targeted interventions to optimise resource deployment and improve healthcare accessibility. Public health policymakers should prioritise investments in urban areas where community health centres demonstrate superior performance, potentially through targeted funding or capacity-building initiatives. Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.