Lymphocytic gastritis (LG) is a rare subtype of chronic gastritis. It is defined as dense proliferation of intraepithelial lymphocytes (IELs) more than 25 lymphocytes per 100 epithelial cells. The known major causes of LG are celiac disease and Helicobacter pylori infection. H. pylori associated LG (HpLG) has more enhanced cytotoxic and apoptotic tendencies than chronic H. pylori gastritis. A 12-year-old girl with postprandial epigastric pain was diagnosed HpLG on endoscopic biopsy. After the 1st eradication therapy, H. pylori bacilli were still found, and urea breathing test was positive. Although the endoscopic finding was partially improved, clinical symptoms and histologic finding were persisted. We could achieve the improvement of clinical symptoms and disappearance of IELs after the 2nd eradication. The discordant of histopathologic and endoscopic improvement occurred after the 1st eradication therapy of HpLG. Therefore the clinical and histopathologic evaluation should be considered as well as endoscopic findings.