Image-based computational fluid dynamics (CFD) studies conducted at rest have shown that atherosclerotic plaque in the thoracic aorta (TA) correlates with adverse wall shear stress (WSS), but there is a paucity of such data under elevated flow conditions. We developed a pedaling exercise protocol to obtain phase contrast magnetic resonance imaging (PC-MRI) blood flow measurements in the TA and brachiocephalic arteries during three-tiered supine pedaling at 130, 150, and 170 % of resting heart rate (HR), and relate these measurements to non-invasive tissue oxygen saturation [Formula: see text] acquired by near-infrared spectroscopy (NIRS) while conducting the same protocol. Local quantification of WSS indices by CFD revealed low time-averaged WSS on the outer curvature of the ascending aorta and the inner curvature of the descending aorta (dAo) that progressively increased with exercise, but that remained low on the anterior surface of brachiocephalic arteries. High oscillatory WSS observed on the inner curvature of the aorta persisted during exercise as well. Results suggest locally continuous exposure to potentially deleterious indices of WSS despite benefits of exercise. Linear relationships between flow distributions and tissue oxygen extraction calculated from [Formula: see text] were found between the left common carotid versus cerebral tissue [Formula: see text] and the dAo versus leg tissue [Formula: see text]. A resulting six-step procedure is presented to use NIRS data as a surrogate for exercise PC-MRI when setting boundary conditions for future CFD studies of the TA under simulated exercise conditions. Relationships and ensemble-averaged PC-MRI inflow waveforms are provided in an online repository for this purpose.