Hypertrophic cardiomyopathy (HCM) is a prevalent cardiomyopathy in children, with variable etiologies, phenotypes, and associated syndromic genetic disorders (GD). The spectrum of evaluation in this heterogeneous population has not been well described. We aimed to describe mortality and medical management in the pediatric HCM population, and compare HCM pediatric patients with GD to those without GD. Children (< 18 years) with HCM from the claims-based Truven Health Analytics MarketScan Research Database for years 2013–2016 were identified. Outcomes, including patient visits, diagnostic tests, procedures, medications, and mortality, were reported across demographic and clinical characteristics. Multivariable negative binomial, logistic, and survival models were utilized to test the association between those with and without GD by outcomes. 4460 patients were included, with a median age of 11 years (IQR 3–16), 61.7% male, 17.7% with GD, and 2.1% who died during the study period. There were 0.36 inpatient admissions per patient-year. Patients with GD were younger [8 years (IQR 1–14) vs 12 years (IQR 3–16) (p < 0.0001)], had more echocardiograms (1.77 vs 0.93) p < 0.0001; and ambulatory cardiac monitoring per year (0.32 vs 0.24); p = 0.0002. Adjusting for potential confounders including age, other chronic medical conditions, procedures, and heart failure, GD had increased risk of mortality [HR 2.46 (95% CI 1.62, 3.74)], myectomy [HR 1.59 (95% CI 1.08, 2.35)], and more annual admissions [OR 1.36 (CI 1.27, 1.45]. Patients with HCM show higher rates of death, admission, testing, and myectomy when concomitant syndromic genetic disorders are present, suggesting that the disease profile and resource utilization are different from HCM patients without GD.