Maternal care facilities in Uganda often face challenges related to system inefficiencies that can impact clinical outcomes for mothers and newborns. A quasi-experimental approach was employed, including data collection from facilities and analysis of pre- and post-intervention measures. Key variables included patient flow, staff training, and resource allocation. The analysis revealed a significant decrease in neonatal mortality rates by 15% (95% CI: -20% to -10%) following implementation of improved care protocols. The findings suggest that systematic improvements in maternal care facilities can lead to substantial reductions in neonatal mortality, highlighting the importance of standardised care systems. Health authorities should prioritise investment in training programmes and infrastructure upgrades at maternal care facilities to further enhance clinical outcomes. Maternal Care Facilities, Quasi-Experimental Design, Clinical Outcomes, Neonatal Mortality Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.