Headaches secondary to atlanto-occipital and atlanto-axial joints are often associated with suboccipital pain and aggravated by lateral rotation of the cervical spine and/or flexion or extension of the cervical spine. They are frequently under-diagnosed using traditional radiological evaluation including plain X-rays, computerized tomographic scan, and magnetic resonance imaging. While the natural history of most acute atlanto-occipital and atlanto-axial joint inflammation is resolution over a 2-to-4-week period with conservative management, however, when chronicity sets in, resolution is difficult to achieve using conservative measures, and interventional pain management procedures may be indicated. This review will describe the anatomy of the upper cervical spine, clinical presentation of atlanto-occipital and atlanto-axial joint involvement, and various modalities of treatment, including conservative and interventional modalities.