In patients with inflammatory bowel disease (IBD), cytomegalovirus (CMV) infections could aggravate the course of IBD but it is difficult to distinguish CMV infection from IBD exacerbation endoscopically. Usually, CMV tends to localize to the colon and other organic involvements were reported very rare in the IBD patients. Herein, we report a case that CMV gastric ulcer complicated with pyloric obstruction in a patient with ulcerative colitis during ganciclovir therapy, which was resolved by surgical gastrojejunostomy with review of literature.