AIM:Neonatal surgery in low-income and middle-income countries has a poorer outcome when compared with high-income countries. This study evaluated the management challenges and outcomes of neonatal surgery before and after the introduction of focused interdisciplinary team management in 2013. METHODS:We retrospectively analysed neonatal surgery undertaken at two referral hospitals in Enugu, south-eastern Nigeria from January 2011 to November 2015. Cases managed prior to July 2013 (group A) were compared with those managed from July 2013 (group B). RESULTS:There were 91 cases (group A, 47; group B, 44). The common neonatal conditions were oesophageal atresia (21), anorectal malformation (18) and intestinal atresia (18). The surgical conditions, birthweight, age at presentation and associated anomalies did not differ in the two groups. The treatment was also similar except in oesophageal atresia, where cardiac banding was added to the temporary gastrostomy in late presenting cases with undernutrition in group B. Postoperative complications occurred in 43 (47.3%) cases (group A, 55.3%; group B, 38.6%; P > 0.05), and the overall mortality was 33 (35.3%: group A, 48.9%; group B, 22.7%: P < 0.05). Causes of mortality were unremitting sepsis (group A, 11; group B, 5), anaesthesia complications (group A, 5; group B, 0) and respiratory complication (group A, 7; group B, 5). Delayed presentation, inadequate facilities and defective health insurance scheme were challenges in the two groups. CONCLUSION:Despite the persisting challenges, co-ordinated team management may result in the modest improvement of outcomes of neonatal surgery in our setting. Addressing these challenges may further improve outcomes.