Chronic graft-versus-host disease is a potentially debilitating complication of allogeneic hematopoietic stem cell transplantation. Due to the direct inflammatory effects of the disease on tissue, and the impact on muscle and bone of the high-dose glucocorticoid immunosuppression used to treat the disease, patients are at risk of developing multifactorial functional impairment. This review outlines the clinical assessment and rehabilitation interventions to manage aspects of the disease that cause the most impairment: involvement of the skin/fascial and cardiopulmonary organ systems, as well as steroid-induced myopathy and bone and joint destruction.