We previously reported the clinical usefulness of the mitral annular plane systolic excursion (MAPSE) to evaluate the left ventricular (LV) function in patients with Kawasaki disease (KD) in the acute-phase. However, the feasibility of the MAPSE z-score has not been evaluated in patients with acute KD. We prospectively studied 60 KD patients without coronary aneurysms. The MAPSE z-scores were calculated using our standard MAPSE data. Brain natriuretic peptide (BNP) was measured as a parameter of LV function. In total, 281 healthy age- and body size-matched subjects were chosen as the control group. The MAPSE z-score decreased in the acute-phase (median value, −1.4) and increased in the convalescent phase (median value, 0.18; P < 0.0001). However, there was no significant difference in the MAPSE z-score between patients in the convalescent phase and the control patients (0.18 vs. 0.02, P = 0.199). Multivariate regression analysis revealed that BNP was an independent predictor of the MAPSE z-score (β = 0.40, P < 0.005). According to the receiver operating characteristic (ROC) analysis, the optimal cutoff value for the MAPSE z-score to judge LV dysfunction was −0.9. The MAPSE z-score is a useful index to evaluate LV function, and the cutoff value of −0.9 can be an indicator to judge LV dysfunction in the patients with acute-phase KD.