Fabry disease, characterized by α-galactosidase A (GLA) deficiency, causes left ventricular hypertrophy (LVH) often mimicking hypertrophic cardiomyopathy (HCM). Differentiating Fabry disease from HCM is crucial, given their therapeutic and prognostic differences. A 42-year-old female diagnosed with HCM with left ventricular outflow tract (LVOT) obstruction was referred to our cardiology department after complaining of exertional chest discomfort. Electrocardiography showed LVH with strained ST segment. Echocardiography showed normal wall motion with asymmetric LVH and systolic anterior motion of the mitral valve with a basal LVOT resting gradient of 71 mmHg. Endomyocardial biopsy (EMB) revealed moderately vacuolated cardiomyocytes under light microscopy. Electron microscopy (EM) revealed abundant accumulation of lamellar bodies within cardiomyocytes. Although LVOT obstruction is common in HCM but rare in Fabry disease, the EMB findings suggested Fabry disease. Subsequent genetic testing identified a heterozygous p.Ala37Val (c.110C>T) GLA variant (NM_000169.3), confirming the diagnosis. The patient was prescribed bisoprorol and cibenzorine, which improved her resting gradient and symptoms, and chaperon therapy was initiated. In this case, the patient’s symptoms mimicked HCM with no clinical evidence of Fabry disease other than the electron microscopic findings. This case highlights the importance of EMB using EM to exclude Fabry disease when asymmetric LVH is seen.