Abstract Gas diffusion layers (GDLs) are one of the main components in proton exchange membrane (PEM) fuel cells. In this paper, the effect of anisotropic thermal conductivity of the GDL is numerically investigated under different operating temperatures. Furthermore, the sensitivity of the PEM fuel cell performance to the thermal conductivity of the GDL is investigated for both in-plane and through-plane directions and the temperature distributions between the different GDL thermal conductivities are compared. The results show that increasing the in-plane and through-plane thermal conductivity of the GDL increases the power density of PEM fuel cells significantly. Moreover, the temperature gradients show a greater sensitivity to the in-plane thermal conductivity of the GDL as opposed to the through-plane thermal conductivity.