Introduction We report a relatively rare case of esophageal leiomyoma in the upper thoracic esophagus enucleated by thoracoscopic procedures. The usefulness of preoperative diagnosis and an adequate surgical approach are described along with a review of the relevant literature. Presentaion of case A submucosal tumor 45 mm in diameter was detected in the upper thoracic esophagus of a 69-year-old man. The tumor was preoperatively diagnosed from histopathological biopsy under endoscopic ultrasound-guided fine needle aspiration. Thoracoscopic enucleation was therefore preoperatively scheduled under the left decubitus position in consideration of the low risk of malignant disease. Histopathological diagnosis of the resected specimen was benign leiomyoma and patient outcomes were good. Discussion The need for preoperative biopsy of esophageal submucosal tumor is a controversial issue. However, preoperative biopsy provided the benefits to decide the operative procedure or confirm adequate resection, and our experience suggested that preoperative biopsy did not adversely influence subsequent enucleation. Conclusion Precise preoperative diagnosis is necessary to avoid excessive surgery when managing esophageal submucosal tumor.