Improvements in performance, reliability and durability as well as reductions in production costs, remain critical prerequisites for the commercialization of proton exchange membrane fuel cells. In this thesis, a computational framework for fuel cell analysis and optimization is presented as an innovative alternative to the time consuming trial-and-error process currently used for fuel cell design. The framework is based on a two-dimensional through-the-channel isothermal, isobaric and single phase membrane electrode assembly (MEA) model. The model input parameters are the manufacturing parameters used to build the MEA:​ platinum loading, platinum to carbon ratio, electrolyte content and gas diffusion layer porosity. The governing equations of the fuel cell model are solved using Netwon’s algorithm and an adaptive finite element method in order to achieve quadratic convergence and a mesh independent solution respectively. The analysis module is used to solve two optimization problems:​ i) maximize performance;​ and, ii) maximize performance while minimizing the production cost of the MEA. To solve these problems a gradient-based optimization algorithm is used in conjunction with analytical sensitivities. The presented computational framework is the first attempt in the literature to combine highly efficient analysis and optimization methods to perform optimization in order to tackle large-scale problems. The framework presented is capable of solving a complete MEA optimization problem with state-of-the-art electrode models in approximately 30 minutes. The optimization results show that it is possible to achieve Pt-specific power density for the optimized MEAs of 0.422 g_Pt/kW. This value is extremely close to the target of 0.4 g_Pt/kW for large-scale implementation and demonstrate the potential of using numerical optimization for fuel cell desig