Despite major advances in neonatal and perioperative care, surgical site infections remain a persistent source of morbidity in neonatal surgery. Compared to older pediatric patients, neonates possess unique physiological vulnerabilities, including immature immune function, underdeveloped skin barriers, and frequent exposure to invasive devices, that heighten infection risk. Reported surgical site infection (SSI) rates range from 2.6% to 12.6%, with the highest incidence observed following abdominal wall defect repair, necrotizing enterocolitis surgery, and colorectal procedures. Staphylococcus is the predominant pathogen, although Gram-negative enteric organisms are frequent in gastrointestinal cases. Evidence guiding prophylaxis is limited; available data suggest that prolonged antibiotic use does not reduce SSI risk and may increase adverse outcomes such as fungal infection or necrotizing enterocolitis. Similarly, standard adult-derived wound classifications and prophylactic frameworks often fail to account for neonatal-specific factors. Prevention strategies must therefore be tailored to the neonatal population, emphasizing appropriate antibiotic stewardship, optimized skin preparation, temperature regulation, and neonatal intensive care unit (NICU) infection control. Future research should focus on defining procedure-specific prophylaxis, neonatal SSI definitions, and multicenter quality improvement efforts to standardize care and reduce infection-related morbidity.