Extended septal myectomy for children and adolescents with hypertrophic obstructive cardiomyopathy (HOCM) is a challenging procedure, and related data are currently limited. Our study objective was to assess the early outcomes in children and adolescents with HOCM after extended septal myectomy. From October 2007 to August 2015, 40 consecutive patients with HOCM underwent transaortic extended septal myectomy in Fuwai Hospital, Beijing, China. Patients clinical data were analyzed retrospectively. Mean age at the time of operation was 11.3 ± 4.3 (0.7–16.7) years. Mean body weight at the time of surgery was 40.8 ± 19.7 (4.3–92.0) kg. After myectomy, mean left ventricular outflow tract gradient decreased from 80.1 ± 33.8 to 14.7 ± 11.5 mmHg and mean degree of mitral regurgitation decreased from 1.9 ± 0.9 to 0.5 ± 0.5 (p < 0.001 for both). Concomitant surgical procedures were required in 13 patients (32.5 %). There was no early death. Residual systolic anterior motion and left ventricular outflow tract obstruction were reported in two and three patients, respectively. Moderate aortic regurgitation was found in one patient during a follow-up of 26.4 ± 15.1 months. Restrictive symptoms were improved in the patients with New York Heart Association functional class I or II. A 15.8-year-old patient died 16 months after operation. A permanent pacemaker was installed in one patient 3 months after operation. Extended septal myectomy is safe and effective in children and adolescents with HOCM, with excellent clinical and echocardiographic outcome at early follow-up.