A rare case of atlantoaxial rotatory subluxation occurred after pediatric cervical spine surgery performed to remove a dumbbell-shaped meningioma at the level of the C1/C2 vertebrae. This case is classified as a post-surgical atlantoaxial rotatory subluxation, but has a very rare morphology that has not previously been reported. Although there are several reports about post-surgical atlantoaxial rotatory subluxation, an important point of this case is that it might be directly related to the spinal cord surgery in C1/C2 level. On day 6 after surgery, the patient presented with the Cock Robin position, and a computed tomography scan revealed a normal type of atlantoaxial rotatory subluxation. Manual reduction was performed followed by external fixation with a neck collar. About 7 months after the first surgery, the subluxation became severe, irreducible, and assumed an atypical form where the anterior tubercle of C1 migrated to a cranial position, and the posterior tubercle of C1 and the occipital bone leaned in a caudal direction. The pathogenic process suggested deformity of the occipital condyle and bilateral C2 superior facets with atlantooccipital subluxation. A second operation for reduction and fixation was performed, and the subluxation was stabilized by posterior fixation. We encountered an unusual case of a refractory subluxation that was associated with an atypical deformity of the upper spine. The case was successfully managed by posterior fixation.