Acute kidney injury is a frequent complication in patients requiring extracorporeal membrane oxygenation. A single-center retrospective analysis from a prospective observational database assessing the incidence of acute kidney injury in children undergoing extracorporeal membrane oxygenation, the use of continuous renal replacement therapy and its association with outcomes was performed. One hundred children were studied. Creatinine was normal in 33.3% of children at the beginning of extracorporeal membrane oxygenation, between 1.5 and 2 times its baseline levels in 18.4% of children (stage I acute kidney injury), between 2 and 3 times baseline levels (stage II) in 20.7%, and over 3 times baseline levels or requiring continuous renal replacement therapy (stage III) in 27.6% of the patients. Eighteen patients were on continuous renal replacement therapy before the beginning of extracorporeal membrane oxygenation, 81 required continuous renal replacement therapy during extracorporeal membrane oxygenation, and 38 after weaning from extracorporeal membrane oxygenation, but none of them did at discharge from the pediatric intensive care unit. Fifty-one children survived to pediatric intensive care unit discharge. Mortality was lower in children with normal kidney function or with stage I acute kidney injury at the beginning of extracorporeal membrane oxygenation than in those with stage II or III acute kidney injury (33.3% vs 58.3%, p = 0.021). Mortality in children requiring continuous renal replacement therapy during extracorporeal membrane oxygenation was 54.3% and 21.1% in the rest of patients (p < 0.01). We conclude that kidney function is significantly impaired in a high percentage of children undergoing extracorporeal membrane oxygenation and many of them are treated with continuous renal replacement therapy. Patients treated with continuous renal replacement therapy have a higher mortality than those with normal kidney function or stage I acute kidney injury at the beginning of extracorporeal membrane oxygenation. Most patients surviving to pediatric intensive care unit discharge recover normal renal function after weaning from extracorporeal membrane oxygenation.