Myocardial ischemia caused by microvascular dysfunction is an important pathophysiologic component of hypertrophic cardiomyopathy (HCM), promoting myocardial fibrosis, adverse left ventricular remodeling, and impacting on clinical course and outcome in HCM patients. The aim of study was to assess the prevalence and clinical significance of myocardial ischemia in children with HCM using 99mTc-MIBI single-photon emission computed tomography (SPECT). Ninety-one children with HCM, median age 13.6 years, underwent SPECT evaluation from 2006 to 2017. Imaging was performed at rest and after maximal exercise. Myocardial perfusion defects were identified in 70 children (76.9%; group I), median age 13.8 years. Fixed perfusion defects were evident in 22 of them, while reversible at rest in 48. In 21 children (23.1%; group II), median age 11 years, myocardial perfusion defects were not detected. Patient demographics, echocardiography, resting electrocardiogram (ECG), 24-h Holter ECG, myocardial fibrosis in cardiovascular magnetic resonance imaging, and cardiovascular events were analyzed and compared between the groups. During follow-up at a median of 8.3 years in children with myocardial ischemia, clinical endpoints occurred more often (47 vs. 5; p = 0.02) and more patients reached a clinical endpoint (28 [40%] vs. 3 [14.3%]; p = 0.036). In children with myocardial ischemia, myocardial fibrosis was observed with greater frequency. Myocardial perfusion defects may reflect an ischemic process which (1) affects the clinical manifestations and (2) is an important predictor of adverse clinical events and risk of death in children with HCM. Myocardial ischemia in HCM patients frequently correlates with myocardial fibrosis.