Hemolysis is common during extracorporeal life support (ECLS). Elevated levels of circulating plasma free hemoglobin (FHb) has been linked to the development of hemoglobinuria nephropathy. Its clinical significance in patients receiving ECLS remains unknown. Medical records of 104 children <3 years old who required ECLS after repair of congenital heart disease were reviewed. Forty-two patients required continuous renal replacement therapy (CRRT) during ECLS (CRRT group), and 62 patients did not (no-CRRT group). For all patients, FHb level and the degree of fluid overload at the end of ECLS predicted the mortality rate during ECLS. Compared with the no-CRRT group, the CRRT group had a higher mortality rate during ECLS, a higher peak FHb level during ECLS, a higher FHb level at the end of ECLS, and more days of ECLS. In the CRRT group, the FHb level at the end of ECLS predicted death during ECLS. In the no-CRRT group, the peak FHb level was associated with a worse renal function. In conclusion, elevated FHb levels were associated with renal dysfunction and death during ECLS in children undergoing cardiac surgery. Further studies are needed to elucidate the cause-effect relationship in our findings.