Solitary juvenile xanthogranuloma (JXG) in the spinal column is extremely rare and there has been no report of such a lesion involving C1 and C2 in English literature so far. Here, we report and characterize the first case of xanthogranuloma of the upper cervical spine. This case report draws attention to the fact that solitary xanthogranuloma should be considered among possible diagnoses of spinal tumor in children and young adults. An 18-year-old female patient presented to the hospital with intermittent pain in the right side of the neck. MRI studies revealed a huge soft tissue mass to the right side of the C1 and C2 vertebras, and osseous destruction can be found in the cervical spine CT scan. Complete surgical removal of the tumor and occipital-cervical instrumentation with autogenous bone graft were performed with no complications. The patient was free of pain immediately after the surgery with intact neurological functions. Follow-up MRI 6 and 12 months after the surgery showed no residue or recurrence of the tumor. Our report and the literature review indicate that isolated JXG does not show any predilections of localization inside the central nervous system. So a solitary xanthogranuloma should be considered among possible diagnoses of spinal tumor in susceptible patients. Localized JXG shows isointense signals in MRI and enhances homogeneously with gadolinium. Immunohistochemical studies can ensure the diagnosis. Whenever possible, total surgical removal alone seems to be curative.