Dealing with neonatal surgery, which nearly invariably entails emergency neonatal surgical scenarios, is the most challenging and complex problem in pediatrics and pediatric surgery. Congenital abnormalities are the most common reason for emergency neonatal surgery. Pakistan and other low and middle-income countries (LMICs) account for over ninety percent of these abnormalities. Objective: Our goal is to examine the factors contributing to the high mortality rate in neonatal surgery among those individuals who didn't have access to the NICU. This will inform our recommendations for the worldwide community and the need for NICU care post-operatively. Method: This prospective research was carried out in PIMS hospital from December 2022 to December 2023. Our center has a 15-bed NICU facility, which is almost negligible compared to the patient load of our center. Two hundred patients who underwent surgery during the study were enrolled in our study. Demographic and clinical data were gathered using a questionnaire, and SPSS 25 was used for analysis. Results: Throughout the study period, 33 of 200 neonates died, resulting in a 16.5% mortality rate. Over 53% of these cases were preterm. The research had a minimum gestation age of 29 weeks and a mean gestational age of 35.54 ± 3.56 weeks. The mean newborn's weight had been 2.41 ± 0.52 kg (range: 1.22–3.5 kg). There were more male babies (67.5%) than females. Anorectal malformation was found in four infants who died following surgery. Gastroschisis was discovered in five infants who died after surgery. Sepsis was the most common cause of death following neonatal surgery, amounting to 84.84% of total deaths. Cardiogenic shock was the reason for expiry in 9.09% of the cases, and 6.06% of the cases had respiratory failure as the cause of death. Gastroschisis and esophageal atresia were associated with the most significant mortality. Conclusions: In underdeveloped nations like Pakistan, surgical infants account for a sizable fraction of the total neonatal death rate, most of which may be avoided with proper perioperative and NICU care. Nevertheless, the national health strategy does not give neonatal surgery the priority it deserves. NICUs should be established countrywide to enhance patient care and decrease the overall mortality rate of pediatric surgery.