In allogeneic hematopoietic stem cell transplantation (allo-SCT) recipients with liver dysfunction, it is often difficult to determine the cause. Several cases of liver dysfunction may be interpreted as chronic graft versus host disease without a definitive diagnosis, resulting in continued immunosuppressive therapy for longer periods. Allo-SCT recipients commonly require frequent red blood cell transfusions during the course of treatment and transplantation, leading to significant iron overload, which could be one of causes of liver dysfunction. Here we report an allo-SCT recipient with chronic deteriorating liver dysfunction due to iron overload, despite maintaining transfusion independence for more than four years. Using magnetic resonance-based liver iron concentration (MR-LIC), iron overload-related liver dysfunction was diagnosed. It drastically improved with monthly phlebotomy and has not recurred following its termination. The observations from our case suggested that iron overload should be recognized as a cause of chronic liver dysfunction even in patients who remain transfusion-independent for several years and that MR-LIC analysis is a useful and reliable method for detecting iron overload and monitoring the effect of iron-reduction therapy.