Objective: This study aims to evaluate the incidence and risk factors associated with sepsis in pediatric patients who underwent congenital heart surgery. Method: A total of 289 patients were prospectively enrolled in this study. Patients were divided into two groups according to the Society of Critical Care Medicine (SSCM) diagnostic criteria as Group I including 28 patients who fulfilled the criteria for sepsis and Group II including 261 patients without diagnosis of sepsis. Demographic information, type of operation, complexity, duration of preoperative hospitalization (>5 days) and intensive care unit (ICU) stay, requirement for mechanical ventilation (MV), history of pulmonary hypertension (PHT), and requirement for emergency surgery, total cardiopulmonary bypass (CPB) and aortic cross-clamp (ACC) times. During the postoperative period delayed sternal closure, duration of mechanical ventilation, the need for reintubation, and need for reoperation were also recorded. Results: The incidence of sepsis was 4.74%. The mortality rate in septic patients was 32%. Factors associated with sepsis were younger age, low body weight, duration of preoperative hospitalization and ICU stay, preoperative requirement for MV, palliative and emergency interventions, history of PHT, prolonged MV, reintubation, and reoperation. Multivariate analysis identified reintubation and duration of MV as the major risk factors for sepsis. Conclusion: Serious infectious problems, such as sepsis, are encountered due to inadequate development of immune resistance mechanisms in pediatric patients. Appropriate preoperative preparation of patients for surgery, reducing the length of stay in the hospital and in the ICU, and reducing the need for reintubation by extubating the patients for an optimal period, would reduce the mortality rate due to sepsis.