Allogenic transfusion of immunocompetent T lymphocytes into an immunodeficient recipient is necessary for the development of graft-versus-host-disease (GVHD). The gastrointestinal tract is one of the most involved organs in human GVHD, and single-cell necrosis with apoptotic change and crypt abscess are characteristic histopathologic features. The thymus is important in immune regulation, and dysregulation of the immune system can be expected once its microenvironment is disrupted. We report the case of a 38-year-old woman with malignant thymoma without transplantation or transfusion history who initially presented with myasthenia gravis and clinically developed a GVHD-like syndrome with characteristic GVHD-like colitis on colonoscopy. We propose that disruption of the thymic microenvironment caused a dysregulated immune system and development of a GVHD-like syndrome.