Purpose: Using flexion/extension magnetic resonance imaging (MRI) with a dedicated positioning device, our purpose was to analyze pathologic cranio‐vertebral joint anatomy and motion in patients with rheumatoid arthritis in comparison to normal patients, and to compare flexion/extension MRI with conventional radiographs (CRs) in patients with rheumatoid arthritis. Material and Methods: The 31 patients with rheumatoid arthritis and 20 healthy subjects included in the study were imaged in an open MRI scanner during flexion/extension. A dedicated positioning device was used. Additionally, we compared flexion/extension MRI with CRs in patients with rheumatoid arthritis. In MRI, the orientation and segmental motion of C0, C1, and C2 were assessed and structure of the dens and amount of pannus tissue were observed. Configuration of the cerebrospinal fluid space and the cord was evaluated in each position. In both MRI and CRs, anterior atlanto‐axial subluxation and vertical dislocation were assessed and sagittal diameter of the dural sac was measured. Results: In the neutral position, C1 of the patients was oriented in a more flexed position in relation to both C0 and C2 compared to that in healthy subjects. The patients had more extension in the upper cervical spine than did healthy subjects. In flexion, atlanto‐axial subluxation was greater in CRs than in MRI. In MRI, the amount of vertical dislocation did not depend on position. In the patients, there was considerably more cord impingement in flexion than in other positions. Conclusion: Evaluation of the rheumatoid cervical spine is optimized using MR images in the neutral, flexed, and extended positions. Measurements and relationships between structures should be compared in all positions. CRs with flexion‐extension views are recommended as the first imaging method.