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A 36-year-old man was admitted to our institute due to the diagnosis of esophageal submucosal tumor detected by a periodical upper gastrointestinal endoscopic examination without any complaint. Thoracoscopic enucleation of the lesion with the preoperative clinical diagnosis of esophageal leiomyoma was performed under general anesthesia in the prone position. After immunohistochemical examination, the pathological diagnosis was leiomyoma. There was no remarkable event during the postoperative hospital stay, and the patient was discharged on the 12th day after surgery. This case report suggests that the prone position might be superior to the left lateral decubitus position in thoracoscopic enucleation of esophageal leiomyoma.