Background/Objectives: Extracorporeal membrane oxygenation (ECMO) has been widely used as a life support technique in COVID-19 acute respiratory distress syndrome (ARDS). The use of anticoagulation during ECMO support remains a topic of debate. The primary aim of this study is to demonstrate the safety and efficacy of using argatroban as an anticoagulant instead of heparin in patients with heparin-associated thrombocytopenia. Methods: 40 patients were enrolled and initially treated with unfractionated heparin for anticoagulation during ECMO, composing the UFH group. Twenty-one of these patients experienced a drop in platelet count to below 100,000 cells/mm3 and, after testing negative for IgG anti-PF4/heparin, the anticoagulation was switched to argatroban, composing the ARG group. Hemorrhagic events were recorded along with blood chemistry parameters. Results: Bleedings were significantly more frequent in the UFH group than in ARG group (58/579 days vs. 21/357 days, p = 0.041). No significant differences were observed in hemorrhagic episodes for each bleeding site, except for tracheal stoma (14 vs. 1, p = 0.011). No differences in activated partial thromboplastin time (aPTT) values were found between the two groups (aPTT 42.65 s vs. 44.70 s, p = 0.443). Linear regression analysis revealed that the platelet count on day 5 was correlated with the initial platelet count but not with the type of anticoagulant used (p = 0.001, CI 0.55, 0.69 and p = 0.078). Linear regression analysis in both groups showed a correlation between the duration of ECMO support and intensive care unit stay for the median aPTT and median platelet count. Furthermore, no major systemic thrombotic events or circuit clotting were observed in this patient cohort. Conclusions: Argatroban seems to be safe in patients with persistent heparin-associated thrombocytopenia undergoing ECMO.