We reviewed the long-term outcome of children with hypertrophic cardiomyopathy (HCM) based on the type. We reviewed the medical records of 100 patients (male 54 female 46) with HCM at our hospital between 1977 and 2015. The survival and cardiac event-free survival rates were calculated by the Kaplan–Meier method. The age at the time of the diagnosis ranged from 0 to 15 years with a median of 8 years. The number of patients with Noonan syndrome and hypertrophic obstructive cardiomyopathy (HOCM), idiopathic HCM (i-HCM), and secondary HCM (s-HCM) was 13, 13, 65, and 9 respectively. A dilated phase of HCM occurred in 24 patients. Nineteen (79 %) of the 24 patients died of heart failure, and two underwent a heart transplantation. Eight (33 %) of the 24 patients had s-HCM. The median age when a dilated phase occurred was 15 years old, and the median interval from the initial diagnosis to the dilated phase was 8 years. The median time from the diagnosis of a dilated phase to death was 1.6 years. Sudden death and implantable cardioverter defibrillator implantations occurred in 6 and 11 patients at around 15 years old, respectively. The 20-year survival rates were as follows: Noonan syndrome 84 %; HOCM 82 %; i-HCM 71 %; and s-HCM 17 %. Overall, the survival rates at 10, 20, and 30 years were 83 % (95 % confidence interval 73–89), 69 % (58–78), and 63 % (50–74), respectively. The overall cardiac event-free survival rates at 10, 20, and 30 years were 57 % (47–67), 39 % (31–50), and 32 % (21–44), respectively. The long-term outcome in children with HCM was poor, and the outcome of s-HCM was very poor. The occurrence of a dilated phase worsened the outcome in HCM patients. Sudden death and d-HCM often occurred at around 15 years old. Display omitted •The overall 30-year cardiac event free survival rate was 32 %.•The long-term outcome in children with hypertrophic cardiomyopathy was poor.•The median age when a dilated phase occurred was 15 years old.•Sudden death often occurred at around 15 years old.•The outcome of secondary hypertrophic cardiomyopathy was very poor.