We aimed to investigate the utility of the isoFSE sequence, one of the variable flip angle 3D fast-spin echo sequences, on 3T-MR for displaying vessel walls and diagnosing vertebrobasilar artery dissection (VAD). We retrospectively evaluated 12 initial and 28 follow-up images from 12 patients diagnosed with either intracranial VAD or carotid artery dissection. The image quality for displaying the vessel wall was scored using a five-point scale (1 poor, 5 excellent) on initial T1-weighted isoFSE images for each region of the arteries. The intracranial artery dissection findings assessed at time points after onset were evaluated on initial and follow-up T1/T2-weighted isoFSE images. For small arteries, including the anterior/posterior inferior cerebellar artery, similar high scores were obtained on both unenhanced and contrast-enhanced T1-weighted isoFSE images (average: 4.7-5.0, p > 0.2). On unenhanced images, dissected vertebral arteries showed significantly lower scores than non-dissected vertebral arteries for both readers (p = 0.017 and 0.015, respectively), but the scores were high (3.9 and 4.0, respectively). Definitive findings of VAD were observed on the initial images except in one case. For all cases, definitive findings were seen on at least one of the initial or follow-up images. Temporal changes in the findings could be observed for all cases. In conclusion, we showed favorable wall visualization on T1-weighted isoFSE images and the utility of follow-up imaging using unenhanced-T1/T2-weighted and contrast-enhanced T1-weighted isoFSE sequences with acceptable scan times, which could promote the regular use of 3D black-blood vessel wall imaging.