Objective: To describe a case of Graves’ disease and co-existent pancytopenia associated with autoimmune vitamin B12 deficiency. While thyrotoxicosis and anti-thyroid drugs can cause pancytopenia, other autoimmune conditions such as vitamin B12 deficiency can occur, leading to severe anemia and pancytopenia. Methods: A 19-year-old female with Graves’ disease treated with methimazole presented with thyrotoxicosis and evidence of pancytopenia. Diagnostic studies included a complete blood cell count (CBC), peripheral blood smears, thyroid function tests, and a bone marrow biopsy. Results: White blood cells were 2.4 × 109/L (reference range [RR], 3.4–9.6×109/L), hemoglobin 7.9 g/dL (RR, 11.6–15.0 g/dL), neutrophil count 1.2 × 109/L, and platelets 84 × 109/L (RR, 157–371×109/L). TSH was <0.01 mIU/L (RR, 0.50–4.30 mIU/L), free T4 was 3.7 ng/dL (RR, 1.0–1.6 ng/dL), and total T3 was 221 ng/dL (RR, 91–218 ng/dL). Due to suspicion for drug-induced pancytopenia, methimazole was discontinued. Three days later, she was hospitalized for a syncopal episode with a further decline in hemoglobin to 6.7g/dL, neutrophils to 0.68 ×109/L, and platelets to 69 ×109/L. Bone marrow biopsy findings showing marrow hypercellularity and hypersegmentated neutrophils suggested vitamin B12 deficiency. Vitamin B12 was <70 ng/L (RR, 180–914 ng/L). Intramuscular vitamin B12 injections were initiated, and pancytopenia resolved within 1 month. Conclusion: Although rarely described in the literature, autoimmune vitamin B12 deficiency can be missed as an underlying etiology for pancytopenia in patients with Graves’ disease. The clinical picture can be further confounded when these patients are treated with anti-thyroid drugs known to cause bone marrow suppression.