The utility of routine transesophageal echocardiography (TEE) to exclude left atrial appendage (LAA) thrombus before atrial fibrillation (AF) ablation in patients treated with nonvitamin K oral anticoagulant (NOAC) therapy is unclear. This single-center retrospective study sought to investigate the incidence of LAA thrombus in patients undergoing routine TEE before AF ablation treated with warfarin or NOAC therapy. We included 937 routine pre-AF ablation TEE procedures performed in patients treated with warfarin (n = 517) or NOAC (n = 420). Patients were anticoagulated without interruption for at least 4 consecutive weeks before the TEE. Patients treated with warfarin had lower LAA velocity and underwent TEE earlier in the study period than those treated with NOAC (p <0.05). The incidence of LAA thrombus was higher in patients treated with warfarin (1.55%, 8 of 517) compared with patients treated with NOAC (0.24%, 1 of 420, p = 0.0473 for difference). No LAA thrombus was identified in NOAC-treated patients with a CHA2DS2-VASC score <5 and in warfarin-treated patients with a CHA2DS2-VASC score <2. TEE-related complications occurred in 3 of 937 procedures (0.3%). In conclusion, LAA thrombus is detected rarely during pre-AF ablation TEE. Treatment with an NOAC is associated with a lower incidence of pre-AF ablation LAA thrombus compared with warfarin.