Jejunoileal atresia is a common cause of neonatal intestinal obstruction with high mortality and morbidity in a low resource setting where surgical care is lacking. Herein, a 4-day-old presented with features of acute abdomen and septicaemia, managed with ileostomy diversion and recovered uneventfully. Back ground Neonatal surgical care and neonatal intensive care is lacking in Uganda while jejunoileal atresia and stenosis are still the most common causes of neonatal intestinal obstruction with high mortality and morbidity in a low resource setting. Herein, we presented a 4-day-old neonate who presented to the emergency department as a referral from distant peripheral hospital with features of acute abdomen and septicaemia. He was resuscitated and an ileostomy diversion created. He recovered uneventfully from the hospital and discharged. However, he passed on upon readmission six weeks later from severe acute malnutrition. Conclusion A high index of suspicious on concomitant intestinal perforation in a neonate presenting with intestinal obstruction and delayed access to surgical care while approaches such as intestinal diversion should be sought carefully to mitigate serious consequences of anastomotic leak from primary bowel repair.