Cardiovascular disease remains one of the most significant causes of death and disability throughout the world. The significant variation between that exist between individuals of vascular structures can limit the precision in which risk profiles can be established for cardiovascular diseases. Considering the cerebral vessels within the circle of Willis, the presence and size of communicating vessels between the major feeding and distribution arteries impact the redistribution of blood within the brain following a stroke. The distribution of blood to the smaller perforating vessels attached to the major vessels has been less widely examined and may further contribute to patient outcomes following a stroke. In this study, we have used a GPU enabled version of the HemePure variant of the HemeLB code to efficiently study a range of parametric variations of the basilar artery and connecting vessels to examine the distribution of flow toward cerebral tissue. A canonical representation of the vascular structures has been used to assist in the generalisation of results for a wider population. The simulation workflow used could be used to generate more personalised flow information for a particular patient given the availability of sufficient quality vascular geometry data. The GPU code used here enables a test case to be run significantly faster and more efficiently than to the equivalent CPU code. When subjected to increasing occlusion fraction, the fractional flow within the perforators was observed to reduce more quickly than the relative flow within the basilar artery. It has also been noted that the presence of increasing occlusion fraction serves to suppress the presence of systolic velocity waveforms within the perforator vessels. In our further discussion of these results, we will emphasise the benefits of understanding an individual’s vascular structures when assessing their stroke risk.