INTRODUCTION: Greater occipital neuralgia is the syndrome of pain and abnormal sensation in its distribution area caused by anatomical nerve entrapment. Patients with greater occipital neuralgia experience not only limited head and neck movement, but also posterior occipital pain. However, treatment options are restricted and usually linked to adverse reaction. CASE PRESENTATION: A 33-year-old ethnic Han woman received structure-based medical acupuncture therapy for greater occipital neuralgia. On the basis of clinical examination, visual analogue scale, and six-point behavioral scale, the patient had rear occipital pain the whole day and felt enormous pressure and was uncomfortable. Visual analogue scale score and six-point behavioral scale score were 9 and 4, respectively. After 4 weeks of structure-based medical acupuncture therapy, the patient reported that the symptoms of pain and stress were greatly improved without any discomfort. CONCLUSION: Structure-based medical acupuncture could greatly alleviate clinical symptoms in patients with greater occipital neuralgia. Moreover, structure-based medical acupuncture is a safe, accurate, and efficient complementary and alternative treatment.