Esophageal gland duct adenomas are extremely rare tumors. Here, we report the case of a 75-year-old Japanese man who had undergone total gastrectomy for advanced gastric cancer. Esophageal gland duct adenoma was incidentally found in the lower esophagus. It appeared to be detached from the site of gastric cancer and was well demarcated without a capsule. Histologic analysis revealed papillary and cystic structures mainly comprising eosinophilic cells with minimum nuclear atypia. Immunohistochemical analysis revealed that the tumor were diffusely positive for the S100 protein with preserved alpha-SMA-positive myoepithelial cell layers and a characteristic cytokeratin expression pattern similar to that in normal esophageal gland ducts (CK5/6+++, CK7+++, CK17+, CK18+, CK19+++, CK20-, HMWCK+++). In addition, differentiation into the terminal duct was confirmed by a combination of mucin staining and immunohistochemical and ultrastructural examinations. This is the first report that refers to the ultrastructural findings of an esophageal gland duct adenoma and describes terminal duct differentiation. We believe that the possibility of an esophageal gland duct adenoma should be considered when diagnosing a ductal or glandular lesion of the esophagus.