We aimed to investigate the incidence of limb amputation due to vascular complications related to extracorporeal membrane oxygenation (ECMO) therapy among survivors and examine its association with long-term mortality in these cases. Data from the National Health Insurance Service database in South Korea were extracted for this population-based cohort study. Adult people who underwent ECMO therapy between 2005 and 2018 were included. ECMO survivors were defined as those who survived for at least 365 days after the initiation of ECMO therapy. A total of 6,968 ECMO survivors were included in the study. Among them, 114 (1.6%) underwent limb amputation within 365 days of starting ECMO therapy. On multivariable Cox regression analysis, the risk of 3-year all-cause mortality was not significantly associated with limb amputation compared with those without limb amputation (hazard ratio: 1.53; 95% CI: 0.89–2.63; P = 0.072). In South Korea, 1.6% of ECMO survivors underwent limb amputation within 365 days after initiating ECMO therapy; however, it was not significantly associated with the 3-year all-cause mortality. Our findings warrant future studies on the impact on the quality of life and morbidity-related implications among patients who undergo limb amputation due to ECMO therapy.