This study investigated patient characteristics in paediatric hospitalisations for hypertrophic cardiomyopathy. We used Nationwide Inpatient Sample, which is the largest all-payer inpatient database in the United States, yielding nationally representative estimates, from 2001 to 2014. ICD-9-CM diagnostic codes identified hospitalisations for patients with hypertrophic cardiomyopathy and <18 years. Outcomes included yearly rate of hospitalisation, death, admission via emergency department, and need for surgery. Predictors of interest were age groups (<1, 1–9, and ⩾10 y/o), sex, and race/ethnicity. Logistic regression modelled associations, adjusted by patient- and hospital-level variables. With 2302 weighted hospitalisations, hospitalisation rates were 0.22 per 100,000 children/year, with higher rates for <1 y/o (0.42) and ⩾10 y/o (0.31). Male-to-female ratios were more prominent in the oldest age group; 2.7:1 in ⩾10 y/o versus less than 1.7:1 for <10 y/o. In-hospital mortality was 1.5%, with highest mortality rates among the <1 y/o (6.3%). Children ⩾10 y/o had 5.59 times higher risk of admission from the emergency department than 1–9 y/o age group. Both ⩾10 and <1 y/o age groups had lower risk of surgical intervention compared to the 1–9 y/o group with odds ratio 0.56 and 0.26, respectively. Black children had higher risk of admission from the emergency department than White children with odds ratio 2.78. A relation between age group and sex was observed, with sex-based differences in prevalence and treatment of hypertrophic cardiomyopathy becoming more pronounced with age. Further studies are needed to clarify mechanisms behind age and racial disparity in hospitalisation, especially admission source.