This study investigated the bony ankylosis of the upper cervical spine facet joints in patients with a cervical spine involvement due to rheumatoid arthritis (RA) using computed tomography (CT) and then examined the characteristics of the patients showing such ankylosis. Forty-six consecutive patients who underwent surgical treatment for RA involving the cervical spine were reviewed. The radiographic diagnoses included atlanto-axial subluxation in 30 cases, vertical subluxation (VS) in 10 cases, VS + subaxial subluxation in 3 cases and cervical spondylotic myelopathy in 3 cases. The patients were classified into two groups, those developing bony ankylosis or not and then the differences in the patient characteristics between the two groups was investigated. Furthermore, cervical spine disorders and surgeries were also evaluated in patients who demonstrated such bony ankylosis. The CT reconstruction image demonstrated bony ankylosis in 12 patients (group BA), and the remaining 34 cases (group NB) showed no bony ankylosis. The level at which bony ankylosis occurred was atlanto-occipital joint (AOJ) in eight cases, atlanto-axial joint (AAJ) in two cases and AOJ, AAJ in two cases. No differences were observed between the two groups (age P > 0.54, gender P > 0.39, duration of RA P > 0.72). There was a significant difference between two groups in the patients showing obvious neurological impairment (P = 0.017). In BA group, arthrodesis or decompression was adapted for a caudal region of bony ankylosis. In conclusion, bony ankylosis of the facet joint of the upper cervical spine was detected in 12 of 46 RA patients with involvement of the cervical spine who thus required surgery. These findings showed that the patients demonstrating such ankylosis showed severe cervical myelopathy. In addition, we suggest that the occurrence of bony ankylosis was a risk factor for instability of AAJ, and subaxial instability or stenosis.