This case report describes a 49-year-old woman who diagnosed with acute myeloid leukaemia (AML) harbouring FMS-like tyrosine kinase 3 (FLT3) mutations developed a severe suspected immune-related enteritis during treatment with gilteritinib for maintenance therapy following allo-hematopoietic stem cell transplantation (HSCT). According to the results of Naranjo probability scale, gilteritinib was defined as a ‘possible’ cause of the adverse drug reaction (ADR). Another suspicious inducement, graft-versus-host disease (GVHD), can not be eluted might represent a limitation in this case. To the best of our knowledge, this is the first report on gilteritinib-induced severe enteritis, and will help physicians to keep vigilant, and detect and deal with timely for the possible ADR.