Headaches are widespread in Western Society; they affect approximately 50% of the adult population in the United States. Headaches can present with a variety of clinical and regional symptoms. Although a headache disorder classification system exists, clinical experience has identified various overlapping causes for headaches. It remains clinically challenging to identify the exact etiology causing headaches. For example, the underlying mechanism of cervicogenic headaches remains elusive, but the upper cervical spine plays a key role. Abnormal upper cervical movement patterns, in combination with muscular dysfunctions, are a possible contributing factor to headaches. The upper vertebral spinal nerves C0-C3 have been correlated with cervicogenic headaches. It has been established that biomechanical dysfunction of the upper cervical spine can contribute to neck pain. The atlas plays a key role in the biomechanical dysfunction in the upper cervical spine. Previously, it has been identified that the relative position of the atlas to the axis correlates with headaches. Additionally, it has been demonstrated that an extended contraction of the homolateral obliquus capitis inferior muscles can result in positional default rotation of the atlas. As managing headaches remains multimodal and challenging, there is enough evidence to support the inclusion of the upper cervical spine to normalize joint position, joint mobility, muscle tonicity, and upright positioning. When recognizing the “upper cervical syndrome” and addressing the functioning of the atlas, clinical outcomes will improve for those treating patients with headaches.