Background: Similar autoimmune processes (defective T-cell function) take place during the pathogenesis of aplastic anemia (AA) and Graves’ disease (GD). Antithyroid drugs used for the management of GD may induce AA and GD may occur following treatment of severe aplastic anemia (SAA). Case presentation: Clinical and laboratory investigations were performed for an 11-year-and-2-month-old girl who was referred for bilateral exophthalmus and abnormal thyroid function tests. She had been diagnosed as having severe acquired AA at the age of 8 years and had been treated with allogenic hematopoietic stem cell transplantation from her healthy human leukocyte antigen-matched sibling donor. Clinical examination revealed a weight of 32.6 kg (−0.88 standard deviation [SD] score); height, 145.7 cm (−0.14 SD score); body mass index 15.5 kg/m2 (−1.01 SD score); heart rate, 110/min; blood pressure, 128/74 mmHg; bilateral exophthalmos and an enlarged thyroid gland. The laboratory workup showed hemoglobin of 11.1 g/dL; white blood cells, 7500/mL; platelets, 172,000/mL; free thyroxine (FT4), 4.80 ng/dL (normal, 0.5–1.51); free triiodothyronine (FT3), 17.7 pg/mL (normal, 2.5–3.9); thyrotropin (TSH), 0.015 mIU/mL (normal, 0.38–5.3); antithyroglobulin peroxidase (TPO) antibody, 61.7 IU/mL (normal, 0–9); antithyroglobulin (TG) antibody, <0.9 IU/mL (normal, 0–4) and thyrotropin (TSH) receptor antibodies 14 U/L (normal, 0–1). Doppler ultrasonography showed diffuse enlargement of the thyroid gland and increased vascularity. She was treated with methimazole (0.6 mg/kg/day). L-thyroxine treatment was also needed (50 μg/day). Thrombocytopenia developed during follow-up. A thyroidectomy was performed for definitive treatment at the 14th month of treatment. Conclusions: The association of hyperthyroidism and AA in the pediatric age group is rare. The long-term use of antithyroid drugs and radioactive iodine should be avoided due to their hematologic toxic side effects.