Previously, water extract of Maclura pomifera plant has been found effective on gastric damage. In this study, pomiferin product was purified from this plant by thin-layer chromatography method and its structure was elucidated by nuclear magnetic resonance methods. Its antiulcer effect was investigated on indomethacin-induced gastric damage in rats. For this study, a total of 36 Sprague Dawley female rats were divided into six groups such as healthy, control, reference, and three treatment groups (n = 6 each). Ranitidine (UlcuranA (R) 25 mg/ml vial) was used as reference. Biochemically, lipid peroxidation, and glutathione levels as well as superoxide dismutase, catalase, myeloperoxidase, and cyclooxygenase isoenzymes activities were measured in stomach tissues. Comparing with healthy group, ulcerative area was observed in control group (only administered to indomethacin group). However, Ulcerative area in stomach tissues of rats administered of all doses of pomiferin and ranitidine showed significant decrease (p < 0.05). Also, there were significant changes at the antioxidant levels (lipid peroxidation, glutathione, superoxide dismutase, and catalase) and some important enzyme activities (myeloperoxidase, cyclooxygenase isoenzymes). We found that pomiferin was effective on gastric damage induced by indomethacin. This effect was thought to be caused by positive changes in the antioxidant system.