In this paper, we study how the magnetohydrodynamic (MHD) pulsatile flow of blood and heat transfer works through a constricted artery with a flexible wall. The human circulatory network consists of veins and arteries that sometimes contain constrictions, allowing the impact of the applied magnetic field on flow fields to be observed. The walls of the flowing medium are considered to be a function of time. The flowing blood is hypothesized as shear‐thinning fluid, emulating Yeleswarapu's viscosity replica. Additionally, we consider the energy equation to understand the impact of a magnetic field on heat transfer rates for such flows. The vorticity transport equation along with the stream function equation is obtained using the vorticity–stream function technique. Numerical solutions of the governing nonlinear MHD equations and energy equation in addition to physically pertinent flow conditions were achieved by adapting a finite difference scheme. Considerable attention has been paid to ensure an accurate comparison between the current and previous results. The two sets of numbers appear to match closely. For an even deeper understanding of the flow and heat transport process, the effects of height of stenosis and diverse physiological parameters on time‐averaged wall shear stress (TAWSS), rate of heat transport, and so on are explored in depth through their graphical depiction. In the vicinity of the constriction, it is observed that the separation becomes longer with increasing constriction height. Higher magnetic force strength leads to a reduction in separation length. Newtonian fluids transfer heat more rapidly in their narrowing regions and downstream than fluids with non‐Newtonian behavior.