The craniovertebral junction defined as the occiput, the atlas, and the axis is a complex bony region that contains vital neural and vascular structures. We report the experience of a single academic institution regarding CT-guided biopsy of this skeletal region. We reviewed all of the CT-guided biopsies performed in our department, completed in the craniovertebral junction. We collected data in regard to biopsy procedures, patients’ vital statistics, and histopathological diagnosis. In total, 16 patients (8M and 8F; mean age 52; range 16–86 years old) were included in this series. In eight patients, the lesions were located in the atlas vertebra (8/16—50%), in six patients in the axis (37.5%), and in two patients in the occiput (12.5%). No complications were observed during or after the procedures. All of the procedures were technically successful. The biopsy was diagnostic in 13/16 patients (81.3%): four metastatic lesions (25%—three breast and one prostate cancers), four multiple myeloma bone lesions (25%), three aneurismal bone cysts (18.8%), one aggressive hemangioma (6.3%), and one pseudogout (6.3%). Moreover, in two-thirds (66.6%) of non-diagnostic histological reports, malignancies were excluded. CT-guided percutaneous biopsy is a safe tool and allows obtaining a histological diagnosis, in most cases, even in the most delicate site of the human skeleton—the craniovertebral junction.