Necrotizing enterocolitis is the most common gastrointestinal emergency in newborns. Its etiology involves bacterial colonization, enteral formula feeding, and hypoxic-ischemic injury. The pathology of necrotizing enterocolitis is characterized by coagulation necrosis and bacterial overgrowth, with limited preventative methods available. In addition to affecting the intestine, this disease has long-term neurological consequences for survivors. Hyperbaric oxygen therapy, a well-established treatment for soft tissue infections and injuries caused by hypoperfusion, may serve as an alternative approach for necrotizing enterocolitis. In this study, a necrotizing enterocolitis model was developed in newborn Sprague–Dawley rat pups through the administration of a hyperosmolar formula, combined with exposure to hypothermia and hypoxia. The rat pups received hyperbaric oxygen therapy sessions at 3 absolute atmospheres for 2 hours each, which were administered over 1 or 2 days. The results demonstrated that hyperbaric oxygen therapy significantly reduced mortality in rats with necrotizing enterocolitis and preserved the number of brain cells in the hippocampus. Additionally, hyperbaric oxygen therapy increased the expression of nitric oxide synthase, intestinal fatty acid-binding protein, and superoxide dismutase 3 in the intestine, and elevated superoxide dismutase 3 levels in the hippocampus. These findings suggest that hyperbaric oxygen therapy not only reduces mortality but also mitigates the severity of intestinal and brain lesions in experimental necrotizing enterocolitis, preserving intestinal cell integrity and enhancing antioxidant mechanisms.