Kawasaki disease (KD) is a common febrile disease in East Asia. Because KD with coronary artery aneurysm (CAA) may predispose to thrombosis, children with KD-associated CAA may need anticoagulation in addition to aspirin. In this report, we describe a 6-year-old girl with KD and CAA who was found to have unexpected warfarin-induced coagulopathy caused by CYP2C9 and VKORC1 genotype variants, which affect warfarin metabolism.