Background: The optimum nutritional support of critically ill neonates is considered an essential aspect of their medical management since they are susceptible to rapid nutritional depletion, loss of fat-free mass, organ failure, delayed wound healing, and diminished immune function in the post-gastrointestinal surgery state. Providing appropriate nutritional support for these high-risk patients is a very complex and critical process accompanied by many potential errors. To the best of our knowledge, this study has been the first attempt investigating the energy and protein adequacy and probable barriers to the achievement of nutritional goals in such patients.Methods: The present study was carried out at Akbar Children’s Hospital in Mashhad, Khorasan Razavi province, Iran, during 8 months in 2019. All the gastrointestinal surgical patients admitted to the neonatal intensive care unit (NICU) for at least 72 h were eligible for enrollment in the study. The information on age, gender, primary surgical diagnosis, route of nutritional support, adequacy of received energy and protein, probable barriers to the achievement of nutritional goals, and clinical outcomes were collected in this study.Results: Totally, 59 eligible neonates were included in the study 59.3% (n=35) of whom were male. Among different methods of nutritional support, enteral nutrition (47.5%) was the most frequently used feeding route. Energy and protein adequacy was observed in 35.5% and 79.7% of the patients, respectively. The fluid restriction was the major barrier to the provision of optimum nutritional support, affecting 38.9% of the patients. Finally, nutritional adequacy was observed to be significantly associated with decreased infection rate and length of hospital stay.Conclusion: While 64.5% of the studied neonates did not receive adequate energy, almost 80% of them had adequate protein intake during their post-gastrointestinal surgery state. The awareness of the fluid restriction and non-availability of calorie-dense solutions as the most frequent barriers to the achievement of nutritional goals may lead to making reasonable and realistic decisions on the customized protocols of the NICU patients as well as medical management and insurance coverage of required nutritional products.