Inflammatory bowel disease (IBD) is an immune-mediated chronic inflammatory intestinal condition. With development of various treatment options for IBD, 5-aminosalicylic acid (5-ASA) agents became the drugs of choice due to high efficacy and low risk of complication, specifically effective at inducing and maintaining remission in ulcerative colitis(UC). Pancytopenia caused by 5-ASA agents, especially by mesalazine, has been rarely reported compared with azathioprine, which is commonly used for glucocorticoid-dependent IBD and known to have risk of bone marrow suppression. In the present report, we describe the case of a 57-year-old woman diagnosed with UC, who developed pancytopenia due to adverse effect of mesalazine after recovery from azathioprine-induced pancytopenia. After withdrawal of mesalazine, the laboratory values consistent with myelosuppression continued for 3 months while pancytopenia from azathioprine remained only for 2 weeks. Since pancytopenia can be fatal due to its risk of severe bleeding and infection, close monitoring of clinical presentation is important when starting mesalazine and laboratory data should be evaluated whenever the patients present related symptoms. Furthermore, we suggest that complete blood cell counts should be considered when resuming mesalazine following the development of pancytopenia from any cause, as routinely recommended for azathioprine use.