Anticoagulation during extracorporeal membrane oxygenation (ECMO) for Coronovirus Disease 2019 (COVID-19) can be performed by direct or indirect thrombin inhibitors but differences in outcomes with these agents are uncertain. A retrospective, multicenter study was conducted. All consecutive adult patients with COVID-19 placed on ECMO between March 1, 2020 and April 30, 2021 in participating centers, were included. Patients were divided in groups receiving either a direct thrombin inhibitor (DTI) or an indirect thrombin inhibitor such as unfractionated heparin (UFH). Overall, 455 patients with COVID-19 from 17 centers were placed on ECMO during the study period. Forty-four patients did not receive anticoagulation. Of the remaining 411 patients, DTI was used in 160 (39%) whereas 251 (61%) received UFH. At 90-days, in-hospital mortality was 50% (DTI) and 61% (UFH), adjusted hazard ratio: 0.81, 95% confidence interval (CI): 0.49-1.32. Deep vein thrombosis [adjusted odds ratio (aOR): 2.60, 95% CI: 0.90-6.65], ischemic (aOR: 1.58, 95% CI: 0.18-14.0), and hemorrhagic (aOR:1.22, 95% CI: 0.39-3.87) stroke were similar with DTI in comparison to UFH. Bleeding requiring transfusion was lower in patients receiving DTI (aOR: 0.40, 95% CI: 0.18-0.87). Anticoagulants that directly inhibit thrombin are associated with similar in-hospital mortality, stroke, and venous thrombosis and do not confer a higher risk of clinical bleeding in comparison to conventional heparin during ECMO for COVID-19.