Survival rates for patients with severe aplastic anemia have greatly improved with the development of better supportive care including transfusion strategies and the availability of anti-fungal agents. However, invasive fungal infection remains the main cause of death and increases mortality in severe aplastic anemia patients. Among invasive fungal infections, mucormycosis is one of the fatal diseases in immunocompromised patients. We report the case of a 72-year-old man with severe aplastic anemia treated with immunosuppressive therapy consisting of rabbit anti-thymocyte globulin, cyclosporine, and steroids. The patient developed pneumonia, which did not respond to broad-spectrum antibiotics or echinocandin anti-fungal agents. The pneumonia rapidly progressed and the patient died of multi-organ failure on day 38 after the start of immunosuppressive therapy. The autopsy findings revealed that multiple organs, i.e., lungs, kidneys, heart, liver, spleen, thyroid, and pancreas, were invaded by fungi, and massive coagulative necrosis and thrombotic vessels were found in those organs. Our cultures of a tissue specimen from the patient's left lung were positive for Rhizomucor. We discuss the current problems related to severe aplastic anemia treatment in Japan.