This paper presents a comparative study of non-Newtonian and Newtonian models of blood. A non-Newtonian incompressible 2-D Navier–Stokes (N-S) solver has been developed using Fasttalk language within the Fastflo environment. It is based on the method of operator splitting with artificial compressibility technique. The Power law and Casson models have been used as the constitutive equations for blood with a hematocrit of approximately 45%. These two non-Newtonian models and the Newtonian model are used to simulate unsteady flow through a hypothetical stenotic geometry over an aperiodic time interval of 1 s. Through comparison of the results of the three models, it was found that the wall shear stress (WSS) distribution over the time interval was comparable for both non-Newtonian models. The peak WSS for the Newtonian model had the lowest value. The peak wall shear stress gradient (WSSG) for the Power law was the highest, followed by the Casson and Newtonian models. Flow characteristics such as higher pressure drop across the stenosis, location and movement of vortex were similar in all three models. Non-Newtonian effects were most significant in the vicinity of the stenosis.