To explore effective and convenient rescue therapy options for coronary artery aneurysms (CAA) with thrombosis in Kawasaki disease (KD). A total of 210 patients with KD between the years 2003 and 2013 were retrospectively reviewed in our institute. 144 of these 210 KD developed CAA, and 10 patients with CAA had associated thrombosis. Thrombosis was confirmed by two-dimensional echocardiograms (2-DE). Laboratory values for CAA were analyzed with and without the thrombus group. The characteristics of CAA were monitored by ultrasound. All patients with thrombus received intravenous (IV) antithrombotic therapy, including urokinase, heparin, and oral warfarin. The effectiveness of antithrombotic treatment was evaluated by measuring the ability to dissolve the thrombus. All thrombi in these patients were preceded by a giant CAA and a history of KD. There are no differences in the blood analyses of both CAA with and without thrombus. Moreover, typical KD symptoms and acute myocardial infarction were not found in CAA with thrombosis. The progression of coronary thrombosis in these patients was arrested by antithrombotic and anti-platelet treatment including low-dose urokinase and heparin. Neither clinical features nor laboratory data could reliably predict CAA associated thrombosis. Therapy with IV anti-thrombus and anti-platelet treatment with low-dose warfarin can effectively dissolve thrombi in KD patients.