Computational fluid dynamics models are increasingly proposed for assisting the diagnosis and management of vascular diseases. Ideally, patient-specific flow measurements are used to impose flow boundary conditions. When patient-specific flow measurements are unavailable, mean values of flow measurements across small cohorts are used as normative values. In reality, both the between-subjects and within-subject flow variabilities are large. Consequently, neither one-shot flow measurements nor mean values across a cohort are truly indicative of the flow regime in a given person. We develop models for both the between-subjects and within-subject variability of internal carotid flow. A log-linear mixed effects model is combined with a Gaussian process to model the between-subjects flow variability, while a lumped parameter model of cerebral autoregulation is used to model the within-subject flow variability in response to heart rate and blood pressure changes. The model parameters are identified from carotid ultrasound measurements in a cohort of 103 elderly volunteers. We use the models to study intracranial aneurysm flow in 54 subjects under rest and exercise and conclude that OSI, a common wall shear-stress derived quantity in vascular CFD studies, may be too sensitive to flow fluctuations to be a reliable biomarker.KEYWORDS cerebrovascular disease, computational fluid dynamics, Gaussian process models, patient-specific models, uncertainty quantification Numerous computational fluid dynamics (CFD) models of human cardiovascular and cerebrovascular physiology are published every year, but few of them make any impact in clinical practice. This inconvenient truth has been blamed on the improper use of CFD solvers, 1 insufficient validation of biomechanics models, 2 and lack of understanding of the clinical decision-making process by the biomedical engineers building the models. 3 One additional explanation is that many "patient-specific" CFD models fail to consider the physiological variability of vascular flow, confounding interpretation of model results and producing overly confident predictions of flow quantities.Patient-specific modelling of vascular flow requires an accurate description of the lumen plus the definition of boundary conditions. The latter is done by measuring patient-specific flow waveforms using either phase contrast magnetic resonance imaging (pcMRI) or ultrasound-based flow measurement techniques. When patient-specific flow measurements are not available, cohort-averaged values of flow from the literature are often used. For example, the small-scale studies 4-6 Int J Numer Meth Biomed Engng. 2020;36:e3271.wileyonlinelibrary.com/journal/cnm