The clinical course of acute myocarditis (AM) in children varies from being asymptomatic to causing sudden cardiac death. The aim of this study was to clarify the clinical characteristics and the long-term outcome of AM in children. We enrolled 24 children (aged from 0.1 to 14.6 years, median 8.4 years), who were diagnosed as AM between 1978 and 2010. The maximum follow-up period was 31 years (median 7 years). We retrospectively investigated their clinical course of AM. We also analyzed survival rate, persistence of decreased left ventricular ejection fraction (LVEF) by two-dimensional echocardiogram (2DE), and persistence of complete atrioventricular block (CAVB) by the Kaplan-Meier method. Furthermore, using univariate analysis we analyzed the factors that influenced the outcome. The survival rate was 86 % (95 % confidence interval (CI), 65-96) at 30 years. The persistence rate of LVEF less than 60 % at 1 month, 1 years, and 3 years was 44 % (95 % CI, 22-68), 36 % (95 % CI, 17-62) and 18 % (95 % CI, 3-59), respectively (n = 16), and the persistence of CAVB at 10 days was 36 % (95 % CI, 14-66, n = 11). In six patients with persistence of wide QRS (>100 ms), there were one acute death, two late deaths, and one orthotopic heart transplantation. The 30-year survival rate for six patients with wide QRS and 17 patients without wide QRS in the late phase was 50 % (95 % CI, 17-83) and 100 % (P = 0.0078), respectively. The factors in the acute phase influenced on the outcome were log creatine phosphokinase (CPK) 4.60 (95 % CI, 1.64-29.26, P = 0.001), appearance of ventricular tachycardia 19.71 (95 % CI, 2.50-399.9, P = 0.005), and LVEF 0.91 (95 % CI, 0.81-0.98, P = 0.015), respectively. The predictors of poor outcome in children with AM were high serum CPK, appearance of ventricular tachycardia and low LVEF in the acute phase, and persistence of wide QRS in the late phase. The long-term survival rate of children without these factors was fair.