Veno-arterial extracorporeal membrane oxygenation (ECMO) is used to support patients with high-risk pulmonary embolism (HR-PE) with cardiogenic shock, but data on mid- and long-term outcomes after reperfusion remain limited. We retrospectively compared outcomes after ECMO with embolectomy, ECMO with thrombolysis, or ECMO alone in patients with HR-PE supported at a tertiary-care hospital (2016–2024). Extracorporeal membrane oxygenation was used in 72 patients with HR-PE; 22 received ECMO with embolectomy, 28 received ECMO with thrombolysis, and 22 received ECMO alone. The median duration of ECMO support was 5 days (interquartile range: 4–6 days). In-hospital complications and support time did not differ significantly between groups. Weaning from ECMO was achieved significantly more often with embolectomy (n = 22, 100%) than with thrombolysis (n = 17, 60.7%) or ECMO alone (n = 8, 36.4%) (p < 0.01). Survival to hospital discharge was highest after ECMO with embolectomy (n = 18, 81.8%), as compared with ECMO with thrombolysis (n = 16, 57.1%) or ECMO alone (n = 4, 18.1%) (p < 0.01). One and 3 year survival was 81.8% and 72.7% after ECMO with embolectomy, 55.7% and 46.4% after ECMO with thrombolysis, and 18.2% and 18.2% after ECMO alone (p < 0.001). Extracorporeal membrane oxygenation with early percutaneous or surgical embolectomy may provide a survival benefit over ECMO alone in patients with HR-PE. Further prospective studies are warranted.