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Background: Atrial fibrillation (AF) is the most common type of cardiac arrhythmia. Totally thoracoscopic ablation (TTA) is a surgical treatment showing a high success rate as a hybrid procedure with radiofrequency catheter ablation to control AF. This study compared the early complications of warfarin and non-vitamin K antagonist oral anticoagulants (NOACs) in patients who underwent TTA. Methods: This single-center retrospective cohort study enrolled patients who underwent planned TTA for AF from February 2012 to October 2020. All patients received postoperative anticoagulation, either with warfarin or a NOAC (apixaban, rivaroxaban, dabigatran, or edoxaban). Propensity score matching was performed for both groups. Early complications were assessed at 12 weeks after TTA and were divided into efficacy and safety outcomes. Both efficacy and safety outcomes were compared in the propensity score-matched groups. Results: Early complications involving efficacy outcomes, such as stroke and transient ischemic attack, were seen in 5 patients in the warfarin group and none in the NOAC group. Although the 2 groups differed in the incidence of efficacy outcomes, it was not statistically significant. In safety outcomes, 11 patients in the warfarin group and 24 patients in the NOAC group had complications, but likewise, the between-group difference was not statistically significant. Conclusion: Among patients who underwent TTA, those who received NOACs had a lower incidence of thromboembolic complications than those who received warfarin; however, both groups showed a similar bleeding complication rate. Using a NOAC after TTA does not reduce efficacy and safety when compared to warfarin.