Esophageal duplication cyst (EDC) is a congenital malformation of the posterior primitive foregut, which mainly occurs in the thoracic esophagus. Here, we describe a 3-year-old Han Chinese boy afflicted with intermittent fever of acute onset and dry cough. Thoracic computed tomography revealed an 10 cm × 5.4 cm × 5.8 cm oval-shaped, cyst-like tumor located in the extrapleural space, extending along the right paravertebral gutter and compressing the trachea forward. An additional small-sized, oval-shaped cyst was identified in the posterior mediastinum, between the esophagus and the spinal column, at the T1 level. During open thoracotomy, under general anesthesia, an opaque, thick-walled, esophageal cyst was revealed not to be in communication with the esophageal lumen or the trachea. This cyst was subsequently resected in an en bloc manner. The small (1-cm) esophageal cyst was left untreated based on a “wait-and-see” policy. Histological analysis showed that the resected cyst was walled by hyperplastic, fibrous tissues and locally lined with gastric mucosa inherent glands. This finding was consistent with a diagnosis of EDC, with ectopic gastric mucosa. The respiratory tract symptoms resolved immediately after the operation. Computed tomography obtained at the 6-month follow-up showed that no disease, residual or recurrence, was present after the resection of the large-sized cyst, and the small-sized cyst remained unchanged in size.