Aplastic anemia is a rare immune-mediated complication of thymoma. Thymomas, especially of the cortical type, have the capacity to generate mature T-cells from their immature precursors. Furthermore, mature intratumorous T-cells have an increased autoantigen-specific potential. We present the case of a 75-year-old patient with an inoperable cortical thymoma who developed aplastic anemia 7 years after the initial diagnosis. The infiltration of the bone marrow by these cells was accompanied by the production of cytokines such as tumor necrosis factor alpha (TNF-alpha) in the microenvironment of bone marrow and in the serum sample. The patient was successfully treated with oral cyclosporine A for 14 months and when she died due to progression of the thymoma, 9 months after the discontinuation of cyclosporine, the aplastic anemia had not recurred.