Abstract Fuel cells are still undergoing intense development, and the combination of new and optimized materials, improved product development, novel architectures, more efficient transport processes, and design optimization and integration are expected to lead to major gains in performance, efficiency, reliability, manufacturability and cost-effectiveness. Computational fuel cell engineering (CFCE) tools that allow systematic simulation, design and optimization of fuel cell systems would facilitate the integration of such advances, allow less heavy reliance on hardware prototyping, and reduce development cycles. CFCE requires the robust integration of models representing a variety of complex multi-physics transport processes characterized by a broad spectrum of length and time scales. These processes include a fascinating, but not always well understood, array of phenomena involving fluidic, ionic, electronic and thermal transport in concert with electrochemical reactions. In this paper, we report on some progress in both fundamental modelling of these phenomena, as well as in the development of integrated, computational fluid dynamics (CFD) based models for polymer electrolyte membrane (PEM) fuel cells. A new rational model for coupled protonic and water transport in PEMS, as well direct numerical simulations of two-phase flow in porous gas diffusion electrodes are discussed. Illustrative applications of CFD-based simulations are presented for conventional fuel cells and novel micro-structured fuel cells. The paper concludes with a perspective on some of the remaining theoretical, experimental and numerical challenges to achieve truly functional CFCE tools.