Hemolysis is a complication of cardiopulmonary bypass (CPB). Carboxyhemoglobin (COHb) and methemoglobin (MetHb) were suggested as potential hemolysis biomarkers. This retrospective study was based on a prospective registry aimed to determine the association of COHb and MetHb levels with hemolysis in pediatric patients <4 years old who underwent cardiac surgery with CPB. Plasma-free hemoglobin (PFH), COHb, and MetHb levels were measured before CPB; every 30 minutes during CPB; and on postoperative days 1, 2, and 3. Patients were classified into hemolysis and nonhemolysis groups based on the maximum PFH levels during CPB. A total of 193 patients were included. No significant difference was observed in the maximum COHb levels during CPB (COHb_CPB) between the hemolysis and nonhemolysis groups (1.2% [interquartile range {IQR} 0.9–1.4%] vs. 1.1% [IQR: 0.9–1.4%]; p = 0.17). The maximum MetHb levels during CPB (MetHb_CPB) were significantly higher in the hemolysis group than in the nonhemolysis group (1.3% [IQR: 1.1–1.5%] vs. 1.2% [IQR: 1.0–1.4%]; p = 0.007). Areas under the receiver operating curves of COHb_CPB and MetHb_CPB were 0.557 (95% confidence interval: 0.475–0.640) and 0.615 (95% confidence interval: 0.535–0.695), respectively. Therefore, the predictive ability of both hemolysis biomarkers during CPB is limited.