Hemodynamic factors may affect the potential occurrence of in-stent restenosis (ISR) after intervention procedure of vertebral artery ostial stenosis (VAOS). The purpose of the present study is to investigate the influence of stent protrusion length in implantation strategy on the local hemodynamics of the VAOS. CTA images of a 58-year-old female patient with posterior circulation transient ischemic attack were used to perform a 3D reconstruction of the vertebral artery. Five models of the vertebral artery before and after the stent implantation were established. Model 1 was without stent implantation, Model 2-5 was with stent protruding into the subclavian artery for 0, 1, 2, 3mm, respectively. Computational fluid dynamics simulations based on finite element analysis were employed to mimic the blood flow in arteries and to assess hemodynamic conditions, particularly the blood flow velocity and wall shear stress (WSS). The WSS and the blood flow velocity at the vertebral artery ostium were reduced by 85.33 and 35.36% respectively after stents implantation. The phenomenon of helical flow disappeared. Hemodynamics comparison showed that stent struts that protruded 1mm into the subclavian artery induced the least decrease in blood speed and WSS. The results suggest that stent implantation can improve the hemodynamics of VAOS, while stent struts that had protruded 1mm into the subclavian artery would result in less thrombogenesis and neointimal hyperplasia and most likely decrease the risk of ISR.