The use of proton exchange membrane fuel cells (PEFC) based power trains and stationary systems has been technically demonstrated but is still far from commercial application. Technical development is still required to reach cost and durability targets, and to this aim, modeling and simulation are useful tools to obtain both better understanding of the fundamental occurring processes and to shorten design-associated costs and time. In this paper, a hierarchical 3D-1D approach is proposed, to overcome the deficiencies of a full 1D approach and the characteristic computational costs of a full 3D approach. The polymeric membrane and catalyst layers are represented by a local 1D model, while channels, gas diffusion layers, and solid electrodes are modeled by a full 3D approach. The model capabilities are first investigated with respect to experimental data by means of a full fuel cell simulation; the main chemical, fluid dynamic, and thermal fields are then analyzed in a straight channel configuration. The proposed 3D/1D model is able to accurately represent PEFC specific phenomena and their physical coupling. It could be then successfully applied to both design and development.