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Background: The outcomes after septal myectomy in young children and infants with hypertrophic obstructive cardiomyopathy (HOCM) are not clear. The study sought to report the outcomes after septal myectomy in young children and infants and identify the mechanisms of residual or recurrent obstruction after surgery. Methods: The authors performed an observational cohort study of children and infants under the age of 14 who underwent septal myectomy for HCOM from January 2013 to December 2020. Mean follow-up among 94.3% (n=50) of hospital survivors was 42.09±24.38 months. Results: In total, 56 children and infants [mean (SD) age, 5.38 (3.78) years; 29 (58.1%) were male] underwent septal myectomy for HOCM. Cumulative survival was 100, 96.6, 93.0, and 81.4% at 1, 3, 5, and 7 years, respectively, among hospital survivors. The incidence of residual and recurrent obstruction was 14.3% (8/56) and 13.0% (6/46), respectively. The mechanisms of residual obstruction were identified as subaortic obstruction caused by inadequacy of previous septal excision in two patients, midventricular obstruction caused by inadequacy of septal excision in five patients, and untreated abnormal papillary muscles in one patient. Recurrent obstruction was caused by isolated midventricular obstruction (n=4) and newly emerged systolic anterior motion (SAM)-related subaortic obstruction combining abnormal mitral valve apparatus (n=2). Residual or recurrent obstruction was associated with age less than 2 years at surgery (OR=6.157, 95% CI: 1.487–25.487, P=0.012) and biventricular outflow obstruction (OR=6.139, 95% CI: 1.292–29.172, P=0.022). Recurrent obstruction was associated with age less than 2 years at surgery (OR=6.976, 95% CI: 1.233–39.466, P=0.028). Conclusions: Septal myectomy is still effective and safe in young children and infants. The rate of residual or recurrent obstruction with diverse causes is relatively high, which is more likely to occur in children aged less than 2 years at surgery and those with biventricular obstruction.