Background Emergency laparotomy is a common procedure with high morbidity and mortality. The aim of this study was to assess if the time of surgery (day versus night and weekend) affects the morbidity and mortality in a low-resource setting. Methods A retrospective study was conducted in 2 university teaching hospitals in Rwanda. Patient characteristics, time of laparotomy, operative details and postoperative outcomes were recorded. Chi-square and Wilcoxon rank sum tests were used to determine factors and outcomes associated with time of surgery. Logistic regression was used to determine factors associated with mortality. Results In 309 patients, who underwent emergency laparotomy, 147 (48%) patients were operated during the daytime, 123 (40%) patients were operated during the night shift and 39 (12%) patients were operated on the weekend. Common diagnoses were intestinal obstruction (n = 141, 46%), peritonitis (n = 101, 33%) and abdominal trauma (n = 40, 13%). The overall mortality rate was 16% with 14% in patients operated during day and 17% in patients operated during night and weekends (p = 0.564). Overall, the morbidity rate was 30% with 27% in patients operated during the day compared with 32% in patients operated during night/weekends (p = 0.348). After controlling for confounding factors, there was no association between time of operation and mortality or morbidity. Conclusion Morbidity and mortality associated with emergency laparotomy are high but the time of day for emergency laparotomy did not affect outcome in Rwandan referral hospitals.