Little information is available concerning the usefulness of electrophysiological confirmation followed by totally thoracoscopic ablation. This study aimed to examine whether postprocedural electrophysiological confirmation is always necessary after totally thoracoscopic ablation (TTA) in patients with isolated persistent atrial fibrillation. Forty-five patients with isolated persistent atrial fibrillation were randomized into 2 groups those who received routine electrophysiological confirmation and additional catheter ablation after totally thoracoscopic ablation (the hybrid group [n = 22]) and those who did not (the TTA group [n = 23]). Electrophysiological study was performed 4 or 5 days after surgery. No early or late mortality occurred. In the hybrid group, 5 patients (23%, 5/22) required additional ablation due to residual potential in the left atrium. At a year postoperatively, normal sinus rhythm was observed in 89% of patients (40/45) and similar in both groups (Odds ratio 0.80, 95% confidence interval 0.32 to 1.99). During follow-up, sinus rhythm was maintained in 16 patients (70%) in the TTA group without additional catheter ablation, which was similar (p = 0.920) to the results in the hybrid group (n = 15, 68.2%). Event-free survival rate at 12 months did not differ between groups (TTA group vs hybrid group, 78% vs 77%; p = 0.633). In simple Cox regression analysis, preoperative left atrium volume index was associated with atrial arrhythmia (p = 0.030, hazards ratio 1.087, 95% confidence interval 1.01–1.18). In conclusion, thoracoscopic ablation provided good 1-year durability in patients with isolated persistent AF irrespective of postprocedural electrophysiological confirmation. Seventy-percent of the TTA group did not need additional catheter ablation.