Allogeneic hematopoietic stem cell transplantation is an effective method for treating various hematological diseases. Membranous nephropathy is the second leading cause of novo glomerular disease after transplantation. Protocadherin FAT1 is a target antigen for diagnosing membranous nephropathy, primarily related to hematopoietic stem cell transplantation. Here we report a rare case of membranous nephropathy after hematopoietic stem cell transplantation. The target antigen of membranous nephropathy was confirmed to be FAT1 by pathology combined with mass spectrometry analysis. The nephrotic syndrome achieved partial remission after corticosteroid combined with cyclosporine treatment, and the patient's condition was stable during follow-up.