Invasive micropapillary carcinoma (IMPC), an aggressive variant of adenocarcinoma, is associated with a poor prognosis. Although IMPC has been reported to occur in various organs, pure IMPC has only been reported in the breast, pancreas and colon. There are no reports of IMPC of the esophagogastric junction (EGJ). According to previous reports on gastric IMPC, IMPC occupied, at most, 90 % of the whole tumor. IMPC is reported to occur least frequently in the gastric cardia. We herein report a rare case of pure IMPC of the EGJ. A 71-year-old male patient presented with epigastric distress. Gastric endoscopy demonstrated an irregularly-elevated lesion of 50 mm in diameter at the EGJ. The patient underwent proximal gastrectomy, resection of the regional lymph nodes and a punch biopsy of the liver. A histopathological examination revealed that almost all of the regions, including the lymph nodes and the sites of liver metastasis, contained IMPC and that a minute region (<1 % of the whole cancer) contained tubular or papillary adenocarcinoma. The further accumulation of pure IMPC cases like the present case would help to elucidate its pathogenesis.