A rare case of isolated right atrial thrombus under anticoagulant therapy for atrial fibrillation is reported herein. The patient was an 81-year-old man undergoing anticoagulant therapy with oral warfarin for atrial fibrillation. During preoperative screening for eye surgery, echocardiography revealed a mobile mass in the right atrium, and emergency hospital admission was indicated. Excision of the right atrial thrombus was performed, and no residual thrombus was detected on postoperative imaging studies. This case was considered a good indication for surgical resection because of potential risk of fatal embolism.