Cardiovascular system abnormalities can result in serious health complications. By using the fluid–structure interaction (FSI) procedure, a comprehensive realistic approach can be employed to accurately investigate blood flow coupled with arterial wall response. The hemodynamics was investigated in both the coronary and carotid arteries based on the arterial wall response. The hemodynamics was estimated based on the numerical simulation of a comprehensive three-dimensional non-Newtonian blood flow model in elastic and rigid arteries. For stenotic right coronary artery (RCA), it was found that the maximum value of wall shear stress (WSS) for the FSI case is higher than the rigid wall. On the other hand, for the stenotic carotid artery (CA), it was found that the maximum value of WSS for the FSI case is lower than the rigid wall. Moreover, at the peak systole of the cardiac cycle (0.38 s), the maximum percentage of arterial wall deformation was found to be 1.9%. On the other hand, for the stenotic carotid artery, the maximum percentage of arterial wall deformation was found to be 0.46%. A comparison between FSI results and those obtained by rigid wall arteries is carried out. Findings indicate slight differences in results for large-diameter arteries such as the carotid artery. Accordingly, the rigid wall assumption is plausible in flow modeling for relatively large diameters such as the carotid artery. Additionally, the FSI approach is essential in flow modeling in small diameters.