Extrapulmonary tuberculosis rarely presents as thyroid involvement along with other manifestations, and poses a diagnostic challenge on account of paucibacillary nature of disease. In general, the diagnosis of tuberculosis is based on epidemiological risk factors, clinical features, imaging studies, in addition to a positive skin testing or Interferon Gamma Release Assay (IGRA). A 14-year boy presented with history of fever and weight loss for one year. On examination, he had painful swelling of fingers and toes along with a painless thyroid nodule and squint. Hand X-ray showed lytic-sclerotic lesions in phalanges. MRI of brian showed multiple ring enhancing lesions and radionuclide thyroid scan showed multinodular goitre. Histology showed epithelioid cell granulomas (thyroid and bone) and tuberculomas of brain confirmed tuberculosis. He responded well to four-drug anti-tuberculous therapy and his fever, squint, thyroid nodule, and dactylitis disappeared. Tuberculosis of thyroid, a rare phenomenon, can be diagnosed and treated well; if clinical index of suspicion is kept high, particularly in tuberculosis prevalent areas.