Carotid artery stenosis (CAS) often requires surgical intervention through carotid endarterectomy (CEA) to prevent stroke. Accurate cerebrovascular risk assessments are crucial in CEA, as poor collateral circulation can lead to insufficient interhemispheric blood flow compensation, resulting in ischemic complications. Therefore, understanding perioperative risk determinants is vital. This study aims to determine the impact of compromised circle of Willis (CoW) morphology on inter-hemispheric blood flow, focusing on indices based on intraoperative internal carotid artery stump pulse pressure and backflow patterns. In 80 CAS patients who underwent CEA, preoperative CT angiography for CoW was conducted. Patients were categorized into five subgroups based on their CoW anatomy and three additional groups based on intraoperative internal carotid artery (ICA) stump backflow patterns evaluated by the surgeon. Continuous blood pressure signals, including systolic, diastolic, mean, and pulse pressure values, were recorded during the procedure. The relationship between CoW anatomical variants and the systolic and diastolic segments of the averaged pressure waveforms, particularly diastolic pressure decay, was analyzed. The correlation between CoW anatomy and stump backflow intensity was also examined. Significant variability in ICA stump backflow and pressure values was evident across CoW variants. Patients with compromised CoW morphology exhibited weaker backflow patterns and lower ICA stump pulse pressure values, consistent with impaired interhemispheric blood flow. Notably, ICA stump diastolic pressure decay was consistent across most CoW variant groups, indicating developed collateral circulation in cases with CoW anomalies. Thus, impaired CoW integrity is associated with compromised interhemispheric blood flow indices based on intraoperative ICA stump pulse pressure and backflow patterns during CEA. Integrating intraoperative pulse waveform analysis with preoperative CT angiography provides a more detailed assessment of cerebrovascular risk, guiding the selective use of shunts. This combined approach may improve surgical outcomes and patient safety by identifying patients at increased risk of perioperative neurological events due to CoW anomalies.