Purpose: Surgical site infections (SSI) contribute to postoperative morbidity and mortality in children. Our aim was to evaluate the prevalence and identify risk factors for SSI in neonates. Methods: Using a defined strategy, three investigators searched articles on neonatal SSI published since 2000. Studies on neonates and/or patients admitted to neonatal intensive care unit following cervical/thoracic/abdominal surgery were included. Risk factors were identified from comparative studies. Meta-analysis was conducted according to PRISMA guidelines using RevMan 5.3. Data are (mean ± SD) prevalence. Results: Systematic review-of 885 abstracts screened, 48 studies (27,760 neonates) were included. The incidence of SSI was 5.6% (1,564 patients). SSI was more frequent in males (61.8%), premature babies (77.4%), and following gastrointestinal surgery (95.4%). Meta-analysis-10 comparative studies (16,442 neonates; 946 SSI 5.7%) showed that predictive factors for SSI development were gestational age, birth weight, age at surgery, length of surgical procedure, number of procedure per patient, length of preoperative hospital stay, and preoperative sepsis. Conversely, preoperative antibiotic use was not significantly associated with development of SSI. Conclusions: Younger neonates and those undergoing abdominal procedures are at higher risk for SSI. Given the lack of evidence-based literature, prospective studies may help determine the risk factors for SSI in neonates.