In Kawasaki disease (KD), endothelial damage and an elevation in coagulant factors provoke thrombosis. Lupus anticoagulant (LA) is strongly associated with the risk of thrombosis in patients with antiphospholipid syndrome; however, there has been no report of positive LA in KD patients. A previously healthy, 2-year-old boy was admitted due to fever, bilateral conjunctivitis, redness of the lips, and unilateral cervical lymphadenopathy. Typical Kawasaki disease was diagnosed on day 5 of illness. Adenovirus antigens were detected in his stool. After the KD symptoms were successfully treated with intravenous immunoglobulin, his activated partial thromboplastin time (APTT) increased to 88 seconds at eight days of illness. The cross-mixing test showed an inhibition pattern, and the presence of LA was proved using diluted Russell's viper venom time. APPT elongation improved due to continued low dose aspirin therapy without thromboembolisms. The possibility of contamination by LA was low because six other patients treated with the same immunoglobulin lot showed no APTT elongation. We speculated that KD-related infections led to the presence of LA, which may have triggered the thrombosis. Further accumulation of data is warranted to elucidate the role of LA in KD patients.