Headache may represent acute phase of intracranial vertebrobasilar artery dissection (iVBAD). We aimed to evaluate its clinical significance in iVBAD. Consecutive acute iVBAD patients were grouped into ruptured iVBAD, unruptured iVBAD with no headache, isolated headache, or concurrent headache with neurological symptoms. Composite hemorrhagic/ischemic endpoints, and dynamic arterial changes were graded. Clinical characteristics of the four groups, and association between headache and composite outcomes was evaluated. Headaches were precedent in 79% of the ruptured iVBAD patients (maximal delay, 10D). In unruptured iVBAD, when patients with no headache (N = 69), concurrent headache (N = 111), and isolated headache (N = 126) were compared, concurrent headache was associated with ischemic endpoints (isolated headache as reference, adjusted odds ratio: 6.40, 95% confidence interval [2.03–20.19]). While there were no differences in hemorrhagic endpoints, dynamic arterial changes were higher in the isolated headache group (aOR: 3.98, 95% CI [1.72–9.18]) but not for the concurrent headache group (aOR: 1.59 [0.75–3.38]) compared to no headache group. Headache was more commonly severe (48.4% vs. 17.3%, p < 0.001) and ipsilateral (59.7% vs. 45.5%, p = 0.03) for isolated headache compared to concurrent headache, indicating a higher causal relationship. In iVBAD, isolated headache may be considered an acute-phase biomarker, associated with dynamic arterial changes.