Spinal tuberculosis accounts for nearly 50% of musculoskeletal tuberculosis cases, but cervical spine involvement is uncommon, occurring in only 3–10%. Tuberculosis of the craniovertebral junction is exceptionally rare and may result in basilar invagination, instability, and severe neurological compromise. Early recognition and appropriate surgical intervention are essential to prevent permanent deficits. We report a case of a 20-year-old male with no known chronic illness who presented with a 2-month history of progressive non-traumatic neck pain and quadriplegia. Neurological examination revealed significant sensorimotor weakness with preserved bowel and bladder function. Magnetic resonance imaging demonstrated basilar invagination with cervicomedullary compression. Chest imaging revealed radiologic findings consistent with pulmonary tuberculosis. The patient underwent posterior decompression with occipitocervical fusion. Intraoperatively, purulent drainage and extensive lytic destruction of the C1 vertebra were identified, instrumented fusion from occiput to C4 was done. Histopathologic examination was consistent with Mycobacterium tuberculosis infection, establishing the diagnosis of atlantoaxial tuberculous osteomyelitis. Postoperatively, neurological improvement was observed, with motor strength graded 4/5 in the bilateral upper extremities and 3/5 in the bilateral lower extremities. Bowel and bladder function remained intact. Antitubercular therapy was initiated, and the patient continues structured physical therapy and rehabilitation with progressive functional recovery. Basilar invagination secondary to atlantoaxial tuberculous osteomyelitis is a rare manifestation of spinal tuberculosis. This case highlights the importance of maintaining a high index of suspicion for tuberculosis in craniovertebral junction pathology. Prompt surgical decompression, stabilization, and targeted antitubercular therapy can result in favorable neurological outcomes.