Tuberculosis is a common disease in India but even then Primary tuberculosis of Thyroid gland is an extremely rare clinical scenario. Diagnosis of this rare disease requires very high level of clinical suspicion as the clinical features have no distinct characteristics and usually mimic with bacterial thyroiditis, thyrotoxicosis, thyroid carcinoma, lymphoma etc. Historically most of patients were diagnosed through histopathology in post operative thyroidectomy specimens. Here we present a case of primary tuberculosis of thyroid which was initially suspected to be a case of deep neck space abscess and was diagnosed by cartridge based nucleic acid amplification test (CBNAAT) through fine needle aspiration cytology (FNAC) of gland.