Our clinical experience led us to realize that craniovertebral junction (CVJ) abnormalities were common in surgical patients with congenital muscular torticollis (CMT). This study aimed to report the concurrence rate of CVJ abnormalities in surgical patients with CMT, along with comprehensive evaluation of type of concurrent CVJ abnormalities. This was a retrospective cohort study in a tertiary hospital, including 41 subjects who underwent surgical release for CMT at the mean age of 8.38 years. The presence of CVJ abnormalities was analyzed, using craniofacial 3-dimensional computed tomography images. The concurrence rate of CVJ abnormalities was 70% in surgical patients with CMT. Subjects with CVJ abnormalities had, on average, 1.48 abnormalities. The CVJ abnormalities were rotation and lateral shift of the atlanto-axial joint along with rotation of atlanto-occipital joint, where rotation of the atlanto-axial joint was most common (82.76%). There is no patient with anterior shift of the atlanto-axial joint. Chronic mechanical tension by the contracted unilateral sternocleidomastoid muscle of CMT could be responsible for concurrent CVJ abnormalities. The CVJ abnormalities are more common in the atlanto-axial joint than in the atlanto-occipital joint. In conclusions, CVJ abnormality seems to be a common concurrent skeletal complication of CMT, at least, in surgical patients. The CVJ abnormality might be included in the list of skeletal complications of CMT. If CVJ abnormalities are significantly more common in surgical patients with CMT, CVJ abnormalities might be one of predictors of surgical patients with CMT.