Intramucosal gastric cancer (IGC) is associated with a very low risk of lymph node metastasis; thus it is the main candidate for minimally invasive surgical procedures, such as endoscopic submucosal dissection (ESD). Herein, we document an extraordinary case of IGC, which showed a very aggressive clinical course. A 66-year-old female underwent ESD for early gastric cancer. Histologically, the tumor consisted mainly of moderately differentiated adenocarcinoma measuring 1.6 cm in diameter, and the tumor was confined to the mucosa. Despite annual esophagogastroduodenoscopic follow-up, the tumor recurred, with wide metastasis to multiple lymph nodes and bones throughout the body after three years. Fluorescence in situ hybridization study demonstrated MET gene amplification as well as low grade polysomy 7 in both original and recurrent tumors. The clinical characteristics of metastatic IGCs and the implication of MET amplification are discussed.