Introduction: Intestinal obstruction is one of the common causes for emergency surgical consultations among neonates. Neonates’ quality of lives can be made better by early identification of the risk factors and proper management. The best available management for NIO is surgical treatment but the success rate for surgery of NIO is not reported as high. There are few studies available worldwide but no research is available in Afghanistan regarding the outcomes and factors associated with NIO surgery.Aim: The current study aims to find the outcome of NIO surgery and associated factors at FMIC, Kabul, Afghanistan.Methodology: A retrospective Case Series design was utilized. Consecutive sampling was employed and with the help of a structured checklist, medical records of 228 patients who had undergone surgery for intestinal obstruction in their neonatal period at FMIC were reviewed from January 2010 to September 2016. Chi-square test of independence was run to determine the factors associated with the outcomes of NIO. Results: A total of 228 neonates were participants of the study. Male to female ratio was 2:1. Mean weight was 3.04 kg and mean age was 9.5 days. Prematurity was seen only in 10 (4.4%) participants. Initially 118 (51.8%) patients were septic at their first visit to FMIC. Overall survival was 85.1% and high mortality was reported in complicated cases. The leading cause of NIO was ARM (42.1%) and leading cause of death was septicaemia (82.4%). Add factors like weight, septic condition at the time of admission, associated anomalies, and specific type of etiologic pathology, diagnostic accuracy and postoperative complications were found to be the predictors of outcomes of surgeries performed for patients with diagnosis of NIO at FMIC. Conclusion: The mortality associated with NIO surgery has improved over the years but still there is significant mortality which could be prevented by early diagnosis, proper management like proper resuscitation and a NICU setting with appropriate equipment and skilled health care professionals