Abstract Background In sub-Saharan Africa, neonatal mortality post-cesarean delivery is higher than the global average. In this region, most emergency cesarean sections are performed at district hospitals. This study assesses maternal predictors for poor neonatal outcomes post-emergency cesarean delivery in three rural district hospitals in Rwanda. Methods This retrospective study includes a random sample of 441 neonates from Butaro, Kirehe and Rwinkwavu District Hospitals, born between 01 January and 31 December 2015. We described the demographic and clinical characteristics of the mothers of these neonates using frequencies and proportions. We assessed the association between maternal characteristics with poor neonatal outcomes, defined as death within 24 h or APGAR < 7 at 5 min after birth, using Fisher’s exact test. Factors significant at α = 0.20 significance level were considered for the multivariate logistic regression model, built using a backwards stepwise process. We stopped when all the factors were significant at the α = 0.05 level. Results For all 441 neonates included in this study, 40 (9.0%) had poor outcomes. In the final model, three factors were significantly associated with poor neonatal outcomes. Neonates born to mothers who had four or more prior pregnancies were more likely to have poor outcomes (OR = 3.01, 95%CI:1.23,7.35, p = 0.015). Neonates whose mothers came from health centers with ambulance travel times of more than 30 min to the district hospital had greater odds of having poor outcomes (for 30–60 min: OR = 3.80, 95%CI:1.07,13.40, p = 0.012; for 60+ minutes: OR = 5.82, 95%CI:1.47,23.05, p = 0.012). Neonates whose mothers presented with very severe indications for cesarean section had twice odds of having a poor outcome (95% CI: 1.11,4.52, p = 0.023). Conclusions Longer travel time to the district hospital was a leading predictor of poor neonatal outcomes post cesarean delivery. Improving referral systems, ambulance availability, number of equipped hospitals per district, and road networks may lessen travel delays for women in labor. Boosting the diagnostic capacity of labor conditions at the health center level through facilities and staff training can improve early identification of very severe indications for cesarean delivery for early referral and intervention.