Thymus neoplasms are frequently related to paraneoplastic autoimmune manifestations. Its most common associations are myasthenia gravis and pure red cell aplasia. Aplastic anemia has been increasingly documented as an initial presentation of thymoma. Nevertheless, its development after successful surgical resection of thymoma is a rare condition. We report a case of a 53-year-old man with severe aplastic anemia preceded by amegakaryocytic thrombocytopenia three years after thymectomy with no signs of disease recurrence. He underwent immunosuppressive therapy with cyclosporine 5 mg/kg/day and prednisone 2 mg/kg/day for six weeks. Considering the availability of a compatible donor, allogeneic stem cell transplantation was carried out. However, the patient died 11 days after transplant. A literature review was conducted, and another ten cases of aplastic anemia, diagnosed three months to four years after thymectomy, were identified. These cases suggest persistence of peripheral self-reactive T lymphocytes even years after tumor definitive treatment.