Background Patients with hypertrophic cardiomyopathy (HCM) often develop myocardial ischemia in association with abnormal blood pressure response to exercise. Vagal nerves mediate cardioinhibitory stimuli, with little knowledge regarding vagal response to myocardial ischemia in patients with HCM. Methods Exercise Tc-99m-tetrofosmin myocardial scintigraphy was performed in 59 HCM patients and 39 controls who had no evidence of cardiac disease. We examined how reversible regional perfusion abnormality and transient left ventricular cavity dilation, a parameter of subendocardial ischemia, are related to vagal modulation as assessed by coefficient of high frequency component variance (CCV HF) on heart rate variability. We then correlated the results with abnormal blood pressure response to exercise, defined as failed increase ≥25 mm Hg during exercise. Results Regional perfusion abnormality and left ventricular cavity dilation were observed in 26 and 21 HCM patients, respectively. The percentage change of CCV HF from before to after exercise was higher in HCM patients with left ventricular cavity dilation than without or controls (5.2 ± 9.8%, −23.5 ± 5.7%, −14.5 ± 5.5%, P = 0.004). By contrast, the change of CCV HF was similar in HCM patients with regional perfusion abnormality, those without, and controls. The change of CCV HF was correlated with exercise-induced increase in systolic blood pressure ( ρ = −0.64, P < 0.001); HCM patients with abnormal blood pressure response were characterized by a higher percentage change in CCV HF (50.0 ± 18.3%). Conclusions Subendocardial ischemia provoked vagal enhancement in patients with HCM, which may be related to the development of abnormal blood pressure response to exercise.