We investigate the effects of temperature‐dependent viscosity variations on the flow and heat transfer characteristics in an artery in the presence of stenosis. The dimensionless governing equations have been solved using the implicit finite difference method. The local skin friction coefficient and the local Nusselt number at the lower and upper walls are found to be stronger with the increase of stenosis. With the change of position of the upper stenosis, the skin friction and the Nusselt number at the lower plate demonstrate distinct characteristics. A remarkable result is that when the viscosity variation parameter is increased, the vortices following the stenosis become smaller in size. Moreover, the size of vortices increases with the increase of stenosis, whereas it is found to decrease owing to the change of position of the upper stenosis.