Background and purpose It is sometimes difficult to diagnose intracranial vertebral artery dissection in patients with headache as the only symptom. Knowledge of the characteristics of the headache would facilitate the diagnosis. In this study, we aimed to clarify the characteristics of intracranial vertebral artery dissection-related headache using our original self-administered questionnaire. Methods Via the questionnaire, we ascertained headache characteristics and investigated whether they differed between two types of unruptured intracranial vertebral artery dissection, headache type and ischemic type, based on analysis of the responses. Then, we tried to validate the consistency of commonly used criteria for intracranial artery dissection by comparing them with our results. Results Thirty-seven patients were analyzed. Our results identified the following seven headache characteristics in patients with intracranial vertebral artery dissection: (i) occurring in the occipitonuchal region (89%); (ii) unilateral (81%); (iii) pulsatile (70%); (iv) of acute onset (70%); (v) severe (73%); (vi) without nausea or vomiting (73%); and (vii) with concomitant clinical symptoms unrelated to ischemia (81%). Comparison of headache characteristics between the two types of intracranial vertebral artery dissection headache showed that the pain was significantly more severe in headache type than ischemic type intracranial vertebral artery dissection ( p = 0.01). Concomitant clinical symptoms occurred significantly more often in ischemic type than headache type intracranial vertebral artery dissection ( p = 0.03). Our results generally satisfied the established headache diagnostic criteria. Conclusion The pain characteristics of headache type and ischemic type intracranial vertebral artery dissection shown in our study may facilitate its diagnosis.