Objective: Surgical closure of ventricular septal defect is still the most common pediatric cardiac surgical procedure. The aim of this study was to define the risk factors of the complications of ventricular septal defect surgery. Methods: We evaluated the preoperative, perioperative, and postoperative data from echocardiography reports, perfusion reports, and clinical, inpatient, and operative notes of all the patients. The following were the outcome variables for this study: in-hospital death; duration of mechanical ventilation in hours; duration of pediatric intensive care unit stay in days; and duration of hospital stay in days. Herein, we report our single pediatric cardiac center experience between October 2015 and October 2018. Results: A total of 108 patients underwent surgical ventricular septal defect closure during the study period. Prolonged pediatric intensive care unit stay, hospital stay and mechanical ventilation time was associated with younger age and low weight. The patients with genetic syndromes had statistically longer mechanical ventilation time (p < 0.001), pediatric intensive care unit stay (p < 0.001), and hospital stay (p = 0.002). Conclusion: Although genetic syndromes did not affect the complication rates, it affected the lengths of hospital and pediatric intensive care unit stays and mechanical ventilation duration. Young age and lower body weight was a risk factor of prolonged hospitalization, prolonged pediatric intensive care unit stay and prolonged mechanical ventilation. Therefore, these situations should be considered in the postoperative follow-up of patients with ventricular septal defect.