Abstract Background No study has specifically investigated the duration of continuous renal replacement therapy (CRRT) in patients who experienced acute kidney injury during extracorporeal membrane oxygenation (ECMO) support. However, there are concerns that prolonged CRRT may be futile. Methods We conducted a retrospective population-based cohort study using Taiwan National Health Insurance Research Database data collected between January 1, 2007 and December 31, 2013. Patients who received ECMO and CRRT during the study period were included. We divided patients into three groups based on the duration of CRRT received: ≤ 3 days, 4–6 days, and ≥ 7 days. The outcomes were all-cause mortality, end-stage renal disease, ventilator dependency, and readmission rate. Results There were 247, 134 and 187 patients who survived the hospitalization in the CRRT for ≤3 days, 4–6 days and > 7 days respectively. Survival after discharge did not differ significantly between CRRT for 4–6 days vs. ≤ 3 days (adjusted hazard ratio [aHR] 1.16, 95% confidence interval [CI] 0.85–1.57), between CRRT for > 7 days vs. ≤ 3 days (aHR 1.001, 95% CI 0.73–1.38) and between CRRT for > 7 days vs. 4–6 days (aHR 0.87, 95% CI 0.62–1.22). The patients who received CRRT for ≥7 days had a higher risk of ESRD than did those who received CRRT for ≤3 days (adjusted hazard ratio [aHR] 3.46, 95% confidence interval [CI] 1.47–8.14) and for 4–6 days (aHR 3.10, 95% CI 1.03–9.29). The incidence of ventilator dependence was higher in the patients with CRRT ≥7 days than in those with ≤3 days (aHR 2.45, 95% CI 1.32–4.54). The CRRT ≥7 days group also exhibited a higher readmission rate than did the 4–6 days and ≤ 3 days groups (aHR 1.43, 95% CI 1.04–1.96 and aHR 1.67, 95% CI 1.13–2.47, respectively). Conclusions Our study found similar long-term survival but increased ESRD and ventilator dependency among ECMO patients who underwent CRRT for ≥7 days. These results offer reason to be concerned that this aggressive life support may maintain patient survival but do so at the cost of long-term disabilities and a lower quality of life.