Although hypertrophic cardiomyopathy (HCM) with an accessory pathway is encountered in clinical practice, there is little evidence of a coherent strategy for ablation of the accessory pathway in patients with HCM. We present the case of a 61-year-old man who had type B Wolff-Parkinson-White (WPW) syndrome with hypertrophic obstructive cardiomyopathy (HOCM). Due to paroxysmal atrial fibrillation, he underwent radiofrequency catheter ablation of the accessory pathway located in the right postero-lateral wall to prevent secondary symptomatic events. His LV dyssynchrony improved after the procedure, but the degree of the LV outflow tract (LVOT) pressure gradient was increased. To stabilize the LVOT pressure gradient, he needed additional medications. This case shows that patients with HOCM should be carefully evaluated before making a decision concerning ablation of the accessory pathway.