A 60-year-old woman with an abnormality discovered during a chest X-ray was referred to the authors' hospital for diagnosis and treatment. Upon enhanced computed tomography (CT), endoscopic ultrasonography, and magnetic resonance imaging, a tumor on the left side of the lower thoracic esophagus was detected. We diagnosed mediastinum cyst. One year after the first visit, a CT examination confirmed an increase in lesion size. Therefore, surgery was performed using a left thoracoscopic approach in the prone position. Before surgery, 3D models were used for simulation. Excision was performed without leakage of the contents. The histopathological diagnosis was a bronchogenic cyst. The left thoracoscopic surgery in the prone position is an uncommon approach but is useful for resecting tumors in the left side of the lower mediastinum. The authors were well-prepared and able to perform safe and reliable surgery.