Although central nervous system complications occasionally accompany during the acute phase of Kawasaki disease, clinically problematic arrhythmia is quite rare. We report a case accompanied by encephalitis and several kinds of problematic arrhythmia. Following the diagnosis of Taussig-Bing anomaly and coarctation of the aorta, the patient underwent aortic arch reconstruction, an arterial switch operation, and ventricular septal defect closure. No significant arrhythmias were observed. At the age of 5 years, the patient presented with a fever, rash, conjunctival hyperemia, and redness of the lips and fingertips. He was subsequently diagnosed with Kawasaki disease. The patient also presented with disorientation, and electroencephalography revealed overall slow-wave activity, indicating encephalitis. The patient received high-dose immunoglobulin and steroid pulse therapy. Sinus arrest was detected on day 10, and an atrial flutter with a 2 : 1 to 4 : 1 atrioventricular conduction block occurred on day 20. Although cardioversion succeeded in alleviating the atrial flatter, the patient experienced significant sinus arrest. The sinus arrest was alleviated 3 days later. Kawasaki disease-induced vasculitis and the arterial switch operation may both have influenced the sinus node dysfunction. Although sinus node function recovered, the possibility of progression into the sinus node dysfunction in the future should be considered.