Kawasaki disease (KD) is classified as a medium-sized vasculitis of systemic vasculitis syndrome characterized by hypercytokinemia. Although the etiology of KD remains unidentified, epidemiological features point to the role of infection and genetic predisposition. Recent studies revealed endothelial damage and resultant thrombin generation, as well as B-cell activation during the acute phase of KD. Several anti-endothelial cell autoantibodies (AECAs) have been identified in KD patients. Taken together with the recently developed concept of immunothrombosis, a potential pathogenic mechanism for KD emerges. First, some polyclonal antibodies generated against invading microorganisms would exhibit cross-reactivity toward endothelial cell components and become dominant during affinity maturation. AECA binding to endothelial cells would cause endothelial activation or damage, with proinflammatory cytokine release, fostering a hypercoagulable state by leukocyte activation by proinflammatory cytokines. This, in turn, would lead to coronary artery lesions. KD vasculitis might be initiated upon AECA binding to the vasa vasorum and progress to panvasculitis and a vulnerable vessel wall, resulting in an aneurysm. The aneurysm would cause flow recirculation and alteration of wall shear stress. Consequently, platelets activated by shear stress, along with ultra-large von Willebrand factor (VWF) released by endothelial cells, would cause platelet-driven arterial thrombosis. Autoimmunity-associated thrombosis initiated by AECA binding to endothelial cells might play a major role in the pathogenesis of certain subtypes of KD. The notion of KD consisting of subtypes, the major one of which is AECA-associated vasculitis, will help facilitate a better understanding of KD and further promote early and accurate diagnosis, which remains challenging.