After alcohol septal ablation (ASA), regression of left ventricular hypertrophy (LVH) has been observed in several studies using echocardiography or cardiac magnetic resonance, and favorable changes of myocardial excitation have been expected. However, no studies have focused on the alteration of electrocardiography (ECG) findings after ASA. Therefore, we evaluated serial changes in ECG parameters during the chronic phase after ASA for drug-refractory hypertrophic obstructive cardiomyopathy (HOCM). From 1998 to 2014, we performed 187 ASA procedures in 157 drug-refractory HOCM patients. After excluding patients who underwent dual-chamber pacing therapy and who underwent staged or repeat ASA within 2 years after the index ASA, 25 patients without bundle branch block and additional pacemaker implantation were enrolled in the main study group. ECGs, echocardiograms, and clinical follow-up data were evaluated at baseline and, 1, 6, 12, and 24 months after ASA. Patients with bundle branch block or additional pacemaker implantation were assigned in a referential group (n = 79), in which the echocardiographic changes between baseline and at 1 year were evaluated. Sokolow–Lyon index (SLi), Cornell index, and total 12-lead QRS amplitude significantly decreased during 2-year follow-up after ASA. SLi and Cornell index significantly decreased from 6 to 12 months (p < 0.05 vs. p < 0.01). Changes in SLi were significantly associated with changes in the interventricular septal thickness (r = 0.54, p < 0.005), left ventricular mass index (r = 0.40, p = 0.050), and peak creatine phosphokinase level (r = −0.41, p = 0.042), but not in the Cornell index and 12-lead QRS amplitude. In the comparison between baseline and at 1 year, significant improvements in the interventricular septal thickness, posterior wall thickness, left atrial size, E/A ratio, and E/e′ were observed in the echocardiographic study. Changes of SLi reflected regression of LVH after ASA with the best correlation. During the chronic phase after ASA, LVH regression was confirmed by echocardiographic and ECG parameters.