Extrapulmonary tuberculosis (TB) is a well-recognized cause of pyrexia of unknown origin. However, clinical presentation of TB in children with isolated hematological abnormalities is extremely rare. Anemia, usually normocytic, normochromic, leukopenia, leukocytosis, thrombocytopenia, thrombocytosis, and monocytosis are more common complications of TB rather than pancytopenia. Only anecdotal case reports and small case series are available in this regard. We are reporting an 18-year-old boy who presented with on and off low-grade fever for 3 months and anorexia and progressive pallor for 1 month. After extensive workup, pancytopenia remained unexplained. Bone marrow (BM) examination revealed caseating granulomas, along with Mantoux positivity and contact with sputum-positive pulmonary TB. He responded favorably to antitubercular therapy (ATT) within 2 months. This report alerts clinicians to be vigilant regarding the rare possibility of BM TB while investigating unexplained pancytopenia, as it is completely reversible with ATT.