Neonatal mortality remains a significant public health concern in rural Uganda, despite efforts to improve child healthcare access and outcomes. A comparative analysis was conducted using logistic regression models with robust standard errors, accounting for geographical variations in CHI coverage and socioeconomic factors. Among the study population, a 15% reduction in neonatal mortality (95% CI: 3-27%) was observed among infants covered by CHI compared to those not covered. The results suggest that Child Health Insurance programmes have a positive impact on reducing neonatal mortality rates in rural Uganda. Policy makers should consider expanding CHI coverage and intensifying community health education initiatives to further reduce neonatal mortality rates. Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.