A 44-year-old male presented with multiple punctate acute infarcts of the vertebrobasilar circulation and a computed tomographic angiogram showing stenosis of the right vertebral origin. A digital subtraction angiogram demonstrated a new intraluminal filling defect at the origin of the stenotic vertebral artery where antegrade flow was maintained. This filling defect was accepted to be an acute thrombus of the vertebral origin, most likely due to rupture of a vulnerable plaque. The patient was treated with intravenous heparin. A control angiogram revealed dissolution of the acute thrombus under anticoagulation and the patient was treated with stenting with distal protection. Diffusion-weighted magnetic resonance imaging demonstrated no additional acute ischemic lesions. We were unable to find a similar report in the English literature documenting successful management of an acute vertebral ostial thrombus with anticoagulation. Anticoagulation might be considered prior to endovascular treatment of symptomatic vertebral stenoses complicated by the presence of acute thrombus.