A woman in her 30s visited our hospital with stool abnormality. Esophagogastroduodenoscopy revealed a depressed lesion on the greater curvature of the gastric antrum. The tumor was diagnosed as a well-differentiated tubular adenocarcinoma based on the analysis of the biopsy specimen. The rapid urease test, histological examination, and serum anti-Helicobacter pylori antibody indicated that the patient was Helicobacter pylori negative. Gastric mucosal atrophy was not evident on esophagogastroduodenoscopy. Complete cure en bloc resection was successfully performed. The tumor was confined to the mucosa (pT1a-M). Immunohistochemistry showed positive CD10, MUC2, and CDX2 expression and negative MUC5AC and MUC6 expression. Thus, the phenotype was diagnosed as the intestinal phenotype. Helicobacter pylori-negative, well-differentiated early gastric cancer with intestinal phenotype has not been previously reported. Here, we report a rare and valuable case of Helicobacter pylori-negative early gastric cancer with intestinal phenotype treated by endoscopic submucosal dissection.