This review aims to evaluate methodological approaches used in studies assessing rural clinics systems in Rwanda. A rigorous search strategy was employed across multiple databases including PubMed, Scopus, and Web of Science. Studies published between and were included if they addressed the impact of rural clinics systems on patient health outcomes in Rwanda. Methodological quality assessment using the Newcastle-Ottawa Scale (NOS) was conducted. The analysis revealed that multilevel regression models effectively captured the complex interplay between clinic-level interventions and patient clinical outcomes, with a significant proportion of variance explained at both individual and healthcare system levels. Multilevel regression analysis provided robust insights into the effectiveness of rural clinics in Rwanda, demonstrating the importance of considering multiple factors simultaneously to understand their impact on health outcomes. Future research should prioritise methodological rigor in assessing rural clinic systems by employing multilevel regression models and validating findings across different settings and populations. Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.