Thoracic duct cysts in the upper portion of the diaphragm are mostly found in the neck and are rarely found in the mediastinum. Thoracic duct cysts should be differentiated from other mediastinal tumors or cysts, and surgical treatment is required to avoid the development of chylothorax if the cyst ruptures. Herein, we report the case of a patient with a thoracic cyst located just above the diaphragm that was treated with surgical resection.