Abstract Background Vertebral artery dissection (VAD) sometimes has no specific symptoms and is difficult to differentiate from other forms of headache. Case presentation A woman in her thirties had a severe, throbbing left-sided headache. A migraine without aura was suspected and zolmitriptan was administered, which alleviated the symptoms. The woman was consequently deemed to have a migraine without aura. Despite the lack of abnormal neurological findings and showed no abnormalities on cranial computed tomography, her symptoms were not typical for migraines and showed little improvement with therapy. She therefore underwent a cranial magnetic resonance imaging (MRI) examination, which revealed VAD, for which she was transferred to the department of neurosurgery for conservative treatment. Conclusion The possibility of vertebral artery dissection should be considered in the differential diagnosis of severe secondary headaches, and prompt diagnosis and treatment based on detailed MRI and magnetic resonance angiography examinations should be performed.