Endoscopic mucosal resection (EMR) was performed for submucosal tumor (SMT)-like lesion of esophagogastric junction in an 81-year-old male. Histopathological findings revealed the presence of adenocarcinoma with high-grade cytological atypia. No foci of Barrett’s esophagus and/or heterotopic gastric mucosa were detected in the specimen. Intraepithelial squamous cell carcinoma was also not detected in the adjacent stratified squamous layer. The contour of the tumor was similar to normal esophageal gland ducts but tumor did have immunohistochemical staining patterns similar to esophageal cardiac glands. Esophageal adenocarcinoma arising in the background without the foci of Barrett’s esophagus is extremely rare and we reported the case with review of the literature in this study.