In railway systems, layered structures could be induced in wheel–rail contact interfaces due to several causes, such as head hardening, work hardening, plastic deformation, and mechanical or thermal excursion-induced phase transformation. This study proposes an explicit finite element (FE) method for investigating elastic layer effects in wheel–rail rolling contact. The proposed method is first validated by comparing its solution with that of Kalker’s boundary element method (BEM) when the layer is not present, with a focus on the tractive rolling contact. To investigate general layer effects, the rail is assumed to consist of two layers, i.e., the top layer and the matrix material. The top layer is assumed to have different elastic moduli from the matrix material and then the top elastic layer effects on contact characteristics such as contact stress, contact patch, and subsurface stress are investigated. Different layer thicknesses are also considered. It is observed that a harder layer tends to introduce larger contact pressure and surface shear stress, but a smaller contact patch. A harder layer also produces larger subsurface stresses. A thicker layer may intensify these effects. The results suggest that in engineering applications, the analysis of wheel–rail rolling contact consequences such as wear and rolling contact fatigue (RCF) may need to consider the layered structures using appropriate methods.