Atherosclerosis in carotid arteries poses significant risks, including plaque embolization and ischemic stroke. While exercise is known to decelerate atherosclerosis in healthy arteries, its effects on stenosed arteries under varying heart rates remain complex. The present study conducts CFD simulations using COMSOL Multiphysics® 5.6 on a 3D carotid artery model to examine the impact of different exercise intensities on arterial hemodynamics. Blood is modeled as a single-phase non-Newtonian fluid obeying the Carreau–Yasuda model. For a baseline male population aged 45 years, target heart rates for moderate and vigorous exercise are calculated using the Heart Rate Reserve (HRR) method, with cardiac cycle times adjusted accordingly to simulate pulsating arterial velocity profiles. The magnitude of flow velocity increase is incorporated based on graded treadmill exercise literature. Hemodynamic parameters, including blood pressure (BP) upstream of plaque deposition and wall shear stress (WSS) in the stenosed and bifurcation regions, are analyzed from the CFD simulations. The simulation results reveal that with higher exercise intensity, healthy arteries show a linear increase in time-averaged pressure (TAP) and a mild increase in time-averaged wall shear stress (TAWSS), preventing plaque deposition. However, in arteries with 50% stenosis, moderate exercise decreases TAP, while vigorous exercise increases both TAP and TAWSS in the stenosed regions, heightening the risk of plaque rupture and ischemic stroke. The study signifies the need for identification of thresholds of risk of plaque rupture using such hemodynamic parameters, and subsequent research into tailored exercise protocols based on stenosis severity.