Multiple cranial nerve palsies frequently accompany hypoglossal nerve palsy, potentially indicating malignancy, such as lymphoma, nasopharyngeal carcinoma, or metastases. However, when solely the hypoglossal nerve is affected, the causes may involve Chiari malformation, arachnoid cyst, or infectious mononucleosis, suggesting a positive prognosis. Craniocervical junction tuberculosis (TB), is an uncommon cause of isolated hypoglossal nerve palsy and has been reported infrequently in the literature. Craniocervical junction tuberculosis accounts for only 0.5% of TB cases overall and 6% of extra-pulmonary TB cases. We present here one such case of a 17-year-old male of Indian origin with a subacute history of tongue deviation and neck pain. Additionally, the patient reported loss of weight and appetite. The patient had significant posterior cervical lymphadenopathy. Neurological examination revealed findings suggestive of right peripheral hypoglossal nerve involvement. Blood investigations showed lymphocytosis along with an elevated erythrocyte sedimentation rate of 45 mm/h and elevated lactate dehydrogenase levels of 325 U/L. Tuberculin skin testing was positive and sputum acid-fast staining confirmed acid-fast bacilli. Magnetic Resonance Imaging of the cervical spine revealed a soft tissue component in the prevertebral space measuring 3.5×4.8 cm with a right paraspinal component adjoining the hypoglossal canal with peripheral contrast enhancement. Histological findings on the lymph node showed granulomatous lymphadenitis, suggestive of tuberculosis. The patient was started on 4-drug anti-tubercular therapy consisting of Isoniazid, Rifampicin, Pyrazinamide, and Ethambutol for a period of 18 months. He was subsequently followed up for 6 months till the resolution of palsy. This case emphasizes the importance of thorough evaluation and a meticulous workup to identify the underlying cause of hypoglossal nerve palsy and the importance of considering tuberculosis as a potential cause of isolated hypoglossal nerve palsy in everyday practice.