Extracorporeal membrane oxygenation (ECMO) is a form of life support for critically ill patients with severe respiratory or cardiac failure. Interactions between patient blood and ECMO biomaterials increase the risk of thrombosis, necessitating concurrent anticoagulation treatment, with the standard of care being heparin. However, hemostatic complications such as thrombosis and bleeding remain prevalent. Activated factor XII (FXIIa) inhibitors are selective anticoagulants and offer a potential alternative to heparin. We aimed to evaluate the efficacy of IMB-F12, a cyclotide-based FXIIa inhibitor, in human blood using an ex vivo ECMO model. Ten circuits were randomly allocated to heparin or IMB-F12 and ran for 6 h. Primary hemostasis was assessed by full blood cell count, aggregometry, flow cytometry, and von Willebrand factor multimer analysis; secondary hemostasis by activated clotting time (ACT), rotational thromboelastometry (ROTEM), prothrombin time, and activated partial thromboplastin time. All circuits ran successfully for 6 h with stable oxygenator resistance (pressure drop, flow). ACT was higher in the IMB-F12 group than in the heparin group (p = 0.008). Significant differences were observed between ROTEM INTEM and HEPTEM in both IMB-F12 (clotting time (CT) p = 0.001, clot formation time (CFT) = 0.0004, maximum clot firmness (MCF) p = 0.03) and heparin (CT p = 0.01, CFT = 0.004, MCF p = 0.02) groups. Collagen- and thrombin receptor activating peptide (TRAP)-induced platelet aggregation were better preserved in the IMB-F12 group (p = 0.004 and 0.005, respectively). In conclusion, IMB-F12 provides an effective alternative to heparin anticoagulation with an improved preservation of collagen- and TRAP-induced platelet aggregation in an ex vivo model.