Myocardial ischemia changes the electrophysiological properties of the myocardium, but it is difficult to detect the abnormalities of depolarization and repolarization noninvasively in patients with coronary artery disease. Depolarization and repolarization abnormalities were retrospectively investigated in 61 patients (48 males and 13 females) with coronary artery lesions (CALs) caused by Kawasaki disease (KD) from 2007 to 2014 using magnetocardiography (MCG). CAL had been diagnosed by selective coronary angiography. The integral value was computed for each channel, and isointegral maps were constructed during depolarization and repolarization. The MCG findings were compared between the stenotic lesions group (SL group) and the non-stenotic lesions group (non-SL group). The incidence of MCG abnormalities was significantly higher in the SL group than in the non-SL group (p < 0.0001). The incidence of abnormal repolarization was significantly higher than that of abnormal depolarization (p < 0.0001). The number of coronary artery occlusions significantly affected the severity of abnormal repolarization (p = 0.02). Six (75%) of the patients with abnormal depolarization had a previous anteroseptal myocardial infarction. The transmural myocardial infarction affects on abnormalities of depolarization, and the non-transmural myocardial infarction might relate on abnormalities of repolarization. The myocardial electrical properties were preserved in patients except very severe coronary stenosis. MCG is possible to detect electrical myocardial abnormalities noninvasively in patients with CALs caused by KD.