Leprosy, caused by Mycobacterium leprae (M. leprae), primarily manifests with cutaneous and peripheral nerve involvement. Systemic involvement, particularly in the bone marrow, is exceedingly rare. This report presents a case of lepromatous leprosy with bone marrow involvement, emphasizing the systemic nature of the disease and the importance of comprehensive diagnostic and management approaches. We aim to present a case of lepromatous leprosy with bone marrow involvement, detailing the clinical presentation, diagnostic evaluation, and management approach. A 65-year-old male with lepromatous leprosy and severe erythema nodosum leprosum developed pancytopenia. After undergoing comprehensive clinical evaluation, including history taking, physical examination, and laboratory investigations, bone marrow examination and molecular diagnostics using polymerase chain reaction (PCR) were performed to confirm the presence of M. leprae as an etiology for his pancytopenia. The bone marrow aspirate revealed hypercellularity with erythropoiesis and thrombopoiesis within normal limits. Foamy histiocytes with erythrophagocytosis were observed, along with the presence of M. leprae on Modified Ziehl–Neelsen stain. Molecular analysis confirmed M. leprae DNA in the bone marrow aspirate. Treatment with multi-drug therapy (MDT) and thalidomide resulted in normalization of blood counts and healing of skin lesions. This case underscores the systemic nature of leprosy and the rarity of bone marrow involvement, highlighting the importance of thorough evaluation in cases of persistent symptoms. Comprehensive diagnostic approaches, including bone marrow examination and molecular diagnostics, are essential for accurate diagnosis and timely initiation of appropriate treatment, ultimately improving patient outcomes and minimizing disease complications.