It is well known that brain natriuretic peptide (BNP) is elevated in the acute phase of Kawasaki disease (KD). We hypothesized that mitral annular plane systolic excursion (MAPSE) could identify LV dysfunction in the acute phase of KD. Fifty patients with KD were enrolled in this study. BNP sampling and an echocardiographic study were performed just before and after intravenous immunoglobulin administration. MAPSE was measured in M-mode in the apical four-chamber view. The %MAPSE was calculated as the MAPSE measured in the acute phase divided by that measured in the convalescent phase. We compared the acute and the convalescent phases of KD. The values of the MAPSE were significantly reduced (45 out of 50 patients) during the acute phase and immediately recovered in the convalescent phase (10.0 ± 1.9 vs. 12.7 ± 1.9 mm, P < 0.0001). Of the parameters tested, %MAPSE was the only echocardiographic parameter that was associated with Log-BNP. Additionally, %MAPSE had a significant negative correlation with Log-BNP (r = −0.45, P < 0.0039). Longitudinal LV contraction is impaired in the acute phase of KD, but it immediately recovers in the convalescent phase. Measuring the longitudinal LV contractility should be essential for evaluating LV function in the acute phase of KD, and MAPSE is useful for this evaluation.