Traumatic atlanto-axial subluxation (AAS) is a rare injury which can be diagnosed by flexion-extension dynamic radiograph on the cervical spine. Here we report on a case of delayed progression of AAS in the chronic phase after a cervical spinal injury. The described case is a 58-year-old man who sustained a closed occipital head injury with subsequent severe tetraparesis and was admitted to our hospital. Although, no obvious bony injuries of the cervical spine were revealed on plain radiograph and CT scan, Magnetic resonance imaging demonstrated intramedullary spinal cord injury at the level of C1-2. In the acute phase, the patient was treated conservatively and the motor dysfunction was well ameliorated. However, the patient gradually suffered again from motor deterioration eight months later and the radiological examinations revealed delayed progression of AAS. After the unsuccessful trial of external reduction for AAS, the patient underwent atlas laminectomy and occipito-cervical internal fixation with compact Cotrel-Dubousset instrumentation. The motor disability improved again after the operation. Sufficient decompression of spinal cord and stable fixation of craniovertebral junction have been obtained for over two years post-operatively. The unique clinical course of the present case is discussed.