This work investigates a two dimensional numerical analysis of blood hammer through the posterior cerebral artery. The non-Newtonian and usual Newtonian blood models are compared in the case of blood hammer through the posterior cerebral artery to quantify the differences between the models. In this way, a validated CFD simulation is used to study non-Newtonian shear-thinning effects of blood. The governing equations for the modeling of two-dimensional transient flow are solved using a combination of characteristics and central finite difference methods, respectively for the hyperbolic and parabolic parts. Herein, the non-Newtonian viscosity characteristic of blood is incorporated by using the Carreau model. To convert the nonlinear terms available in the characteristics equation into the linear ones, the Newton–Kantorovich method is implemented. The verification and validation of the numerical results are carried out in detail. Hemodynamic characteristics of blood hammer through the posterior cerebral artery are derived with both the Newtonian and non-Newtonian models, and the results are meticulously compared and discussed. The results show that when blood hammer occurs, the non-Newtonian properties greatly influence the velocity and shear stress profiles. At the early stages of blood hammer, there is a 64% difference between magnitudes of wall shear stress in these two models, and the magnitude of the wall shear stress for the shear-thinning blood flow is lower than the Newtonian one.