A 17-year-old young man visited our hospital because of severe upper abdominal pain and was diagnosed with acute peritonitis caused by gastrointestinal perforation. Emergent surgical treatment was performed, and the perforated lesion of the stomach was repaired. He recovered and was discharged without any complication at 14 days postoperatively. However, he had intermittent fever 2 days after discharge and visited our hospital again. He was diagnosed with infectious mononucleosis (IM), derived from Epstein-Barr virus (EBV) initial infection, on biochemical examination that was positive for anti-EBV VCA-IgG and negative for EBV nuclear antigen, although he was ameliorated conservatively. This pathophysiology raised a possibility that EBV infection had induced acute gastritis or gastric ulcer leading to the penetration of the stomach. Six weeks postoperatively, esophagogastroduodenoscopy showed a gastric ulcer in the vestibular part of the stomach. Pathologic examination of the stomach revealed mucosal erosion with B-cell infiltration into the lamina propria;however, Epstein-Barr viral infection was unclear by EBV-encoded small RNA in situ hybridization. Here, we report a rare case of gastric perforation that occurred during the incubation period of IM with a review of the relevant literature.