Esophageal duplication cyst is a rare congenital esophageal anomaly of the foregut. This cyst usually occurs in isolation, and thus far, was treated by enucleation through thoracoscopic or thoracotomic surgery. Here we report a case of multiple esophageal duplication cysts that showed different pathological findings, i.e., the cysts were lined with pseudostratified ciliated columnar and stratified squamous epithelium. Esophageal cysts were incidentally detected in a 53-year-old man during the treatment of pneumonia. In chest-computed tomography, the cysts showed a thin wall and homogeneous inner density, while in endoscopy, no communication with esophageal mucosa was observed. We resected the esophageal cysts with endo-staplers under thoracoscopic surgery. No postoperative complications, including esophageal mucosal injury, occurred. A follow-up chest computed tomography revealed the complete resection of the cysts.