Azathioprine is one of the main drugs in the treatment of inflammatory bowel disease (IBD). It has been widely used in the remission and maintenance treatment of IBD. Some patients may experience some degree of myelosuppression, but very few patients experience severe myelosuppression. Here, we report a 20-year-old male Asian patient with severe myelosuppression due to azathioprine treatment of IBD. In this case, the azathioprine-related genotyping test showed that homozygous wild-type TPMT*3 but a c.415C>T homozygous mutation was found in NUDT15. Our report strengthens the association between genetic polymorphisms of azathioprine-metabolizing enzymes and severe myelosuppression. Therefore, we recommend routine NUDT15 c.415C>T phenotype testing prior to long-term azathioprine treatment to avoid severe myelosuppression.