It is difficult to accurately predict treatment resistance in Kawasaki disease (KD). Patients considered to be low-risk cases often develop resistance to intravenous immunoglobulin (IVIG). We herein examined whether information from the clinical course of KD could improve the prediction accuracy of a previously reported risk score. We retrospectively reviewed the clinical records of 100 KD patients. The clinical characteristics and laboratory data were compared between IVIG-sensitive and IVIG-resistant patients and also between patients with and without coronary artery aneurysm (CAA). The total incidence of IVIG resistance and CAA development was 34 and 13 %, respectively. Multiple regression analysis identified the early appearance of principal symptoms (≤day 2 of the illness) as a risk factor for IVIG resistance (OR 2.88, 95 % CI 1.11–7.44, p = 0.0041), whereas delayed IVIG administration (≥day 6) (OR 2.23, 95 % CI 0.66–7.64, p = 0.018) and IVIG resistance (OR 9.05, 95 % CI 2.27–36.10, p = 0.015) were independent predictors for CAA development. The addition of the first appearance day of principal symptoms into a previously reported scoring system improved its prediction accuracy for IVIG resistance. KD patients who had presented with any principal symptoms within 2 days of fever onset were at a high risk for IVIG resistance regardless of previously reported risk score. A careful medical history-taking that is focused on the clinical course enables a better prediction of IVIG resistance.