Headache is a common symptom of cervical artery dissections (CAD). Sometimes, it can be the only symptom and mimic migraine. We aimed to investigate headache characteristics and previous history of migraine in CAD patients, and to compare headache features between patients with internal carotid artery dissection (ICAD) and vertebral artery dissection (VAD). We investigated 53 CAD patients (n = 28 with ICAD, n = 25 with VAD). Demographic and clinical data were evaluated retrospectively. Headache information was obtained from the patient interviews with a structured questionnaire (based on the International Headache Society criteria). The patients with headache were assessed by headache specialist with a face-to-face interview. Headache was evaluated according to International Classification Committee of the International Headache Society ICHD. Headache (n = 38, 71.7%) was the most common symptom in CAD patients, which was mostly thunderclap, throbbing, intense and ipsilateral to dissection. Headache frequency and neck pain were significantly higher in VAD patients (p = 0.002, p < 0.001, respectively). Photophobia and phonophobia were also more common in patients with VAD (p < 0.001, p < 0.001, respectively). 29 (54.7%) of CAD patients had a prior history of headache, that 20 (37.7%) of them met the migraine criteria. CAD should be considered in patients with severe unilateral throbbing headache with phonophobia and photophobia, even in patients with a history of migraine. Phonophobia and photophobia may be more common symptoms in VAD patients. Because headache commonly precedes the development of cerebral ischemic events, it needs prompt and accurate diagnosis and treatment.