Background: Rwanda has registered tremendous achievements in the health sector. However, neonatal morbidity remains high in some areas. This study aims to determine the prevalence and predisposing factors of neonatal morbidity in the Gicumbi District. Methods: The study was a retrospective, cross-sectional study. Overall population of interest comprised 349 neonates. Quantitative data were collected using a pre-tested data extraction tool which comprised of general characteristics of mothers and neonates, social factors, medical insurance and physiological factors. Results: The study found that the prevalence of neonatal morbidity is 28.4%. Bivariate analysis shows that 8 variables were statistically significant with neonatal morbidity. In multivariable analysis, factors identified as statistically associated with neonatal morbidity were mothers who did not have any antenatal care during pregnancy (AOR = 5.3; 95% CI = −1.313–22.118, P < 0.019). Conclusion: Prevalence of neonatal morbidity was significant among neonates born in Gicumbi District and mothers who did not have any antenatal care during pregnancy are most vulnerable. Thus, public health staff, leaders at the facility, and national level are advised to assess all barriers and enablers of Antenatal care coverage.