Cervicogenic headache (CGH) is a prevalent secondary headache disorder associated with upper cervical spine dysfunction, often involving nociceptive convergence at the trigeminocervical complex. While manual therapy and exercise have demonstrated benefit, autonomic dysregulation may contribute to persistent symptoms. This case report explores the integration of external vagus nerve stimulation (eVNS) into a multimodal physical therapy approach targeting both mechanical and neurophysiological contributors to CGH. A 63-year-old female presented with chronic CGH characterized by right-sided suboccipital and supraorbital pain, impaired sleep, and postural dysfunction. Examination revealed a right rotational atlas positional fault, restricted left atlantoaxial (AA) mobility, suboccipital hypertonicity, and reduced deep neck flexor endurance. Initial treatment emphasized manual therapy to restore AA mobility and atlas symmetry, combined with postural correction and neuromuscular training. After initial symptom improvement plateaued, eVNS targeting the auricular branch of the vagus nerve was introduced to modulate autonomic tone. The patient used a handheld eVNS device nightly over three weeks. Substantial improvements were observed in the Neck Disability Index (↓77%), Headache Disability Inventory (↓72%), and pain scores (↓100%). Cervical mobility, atlas symmetry, and deep neck flexor endurance improved markedly. The patient reported reduced anxiety, improved sleep, and sustained headache relief at one-month follow-up. This case highlights the potential synergistic benefits of integrating eVNS within a physiotherapy-led CGH management plan. Further research is warranted to explore its role in targeting autonomic imbalance and enhancing conservative treatment outcomes.