Background: The craniovertebral junction is a complex region, connecting the occiput, the atlas, the axis, and the containing vital neural and vascular structures. There is a great variability in diseases involving the craniovertebral junction, of different nature, each rare in frequency. Methods: We conducted a retrospective chart review of the patients diagnosed with extremely rare pathologies of the craniovertebral junction that we have operated in the last 5 years. Results: After excluding the relatively more frequent pathologies, we identified nine cases of rare craniovertebral junction pathologies. Six were operated using an endoscopic endonasal approach, two using a far lateral transcranial approach, and one underwent a C1 hemilaminectomy. Conclusions: Diagnosis and management of the rare pathologies of the craniovertebral junction are challenging. A multidisciplinary approach is recommended for the proper management of these patients.