Background: Neonatal surgery is extremely challenging and has negligible margin of error. Neonatal surgical conditions account for 11% of the Global Burden of Diseases but the burden of neonatal surgical diseases in Africa is not well documented. Report shows a significant geographical variation both worldwide and within African countries but the outcome and associated factors of surgical neonates has not been studied in neonates admitted to Hawassa specialized compressive hospital. Objective: The aim of this study was to assess the outcomes of surgical neonates and to study the factors associated among those admitted to NICU in Hawassa University Comprehensive Specialized Hospital from January 2018 to January 2022. Methodology: Hospital-based retrospective cross-sectional study was conducted in NICU in 201 neonates from July to August 2022. Non-probability sampling techniques were used to enroll a total of 349 study subjects but only 201 fulfilled the inclusion criteria. Data was collected by trained data collectors using a structured questionnaire from the patients’ cards and NICU registration books. Data was entered, processed, and analyzed using SPSS version 26; Logistic regression was used to identify the factors associated with Neonatal surgical outcomes. Statistically, significance was declared at p <0.05. Result: A total of 201 neonates were evaluated and based on the outcome, patients were divided into 2 groups (Survival n= 168 and Mortality n=33). Incidence of NSM in this study was 16.4%. Factors identified as predictors of NSM were sepsis prior to surgical intervention (AOR: 1.61, 95% CI [0.10, 0.375]; p=0.03), Temperature after surgery (AOR: 1.189, 95% CI [0.101, 0.354]; p=0.00), being delivered out-born (AOR: 1.240, 95% CI [0.051, 0.826]; P=0.040) and site of surgery (AOR: 2.134, 95% CI [1.24, 8.94]; P=0.009). Conclusion: NSM was largely dependent on Preoperative, intraoperative and postoperative variables. Neonatal surgery has a negligible margin of error and warrants expertise to minimize the unwanted outcomes.