This work presents the use of non-commercial software for the design and development of a multiphysics model for some aspects of a proton exchange membrane fuel cell's (PEMFC) operation and performance. Developing the model this way gives users greater freedom to adjust and improve upon the model than with common commercial modeling software packages. By using the non-commercial partial differential equation (PDE) solver FreeFem++, which utilizes a high-level programming language based on C++, we developed a model in which the set of equations representing the mechanisms that govern PEMFC operation and the algorithms for solving it can be freely tweaked, updated or overhauled by users. We discuss our choice of software and describe the advantages and limitations of our modeling approach, such as the flexibility provided by its open nature at the cost of added programming complexity compared to commercial packages. We also note how the geometry of the cell being modeled can easily be controlled through a set of user-defined parameters, or scripted to change for successive model runs as part of an optimization procedure or sensitivity analysis. We present results from a two-dimensional model for the cathode side in order to demonstrate the practicality of this approach.