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Aim: We examined the effect of modulating the shear stress (SS) profile using forearm warming and cooling on subsequent endothelial function in the brachial artery (BA) during exercise. Methods: Twelve healthy young subjects immersed their right forearm in water (15°C or 42°C) during a leg cycling exercise at 120–130 bpm for 60 min. The same exercise without water immersion served as a control. The BA diameter and blood velocity were simultaneously recorded using Doppler ultrasonography to evaluate the antegrade, retrograde, and mean shear rates (SRs, an estimate of SS) before, during, and after exercise. The endothelial function in the right BA was evaluated using flow-mediated dilation (FMD) (%) using two-dimensional high-resolution ultrasonography before (baseline) and 15 and 60 min after exercise. Results: During exercise, compared with the control trial, higher antegrade and mean SRs and lower retrograde SRs were observed in the warm trial; conversely, lower antegrade and mean SRs and higher retrograde SRs were observed in the cool trial. At 15 min postexercise, no significant change was observed in the FMD from baseline in the warm (Δ%FMD: +1.6%, tendency to increase; p = 0.08) and control trials (Δ %FMD: +1.1%). However, in the cool trial, the postexercise FMD at 60 min decreased from baseline (Δ%FMD: −2.7%) and was lower than that of the warm (Δ%FMD: +1.5%) and control (Δ%FMD: +1.2%) trials. Accumulated changes in each SR during and after exercise were significantly correlated with postexercise FMD changes. Conclusion: Modulation of shear profiles in the BA during exercise appears to be associated with subsequent endothelial function.