Abstract The transient behavior of a proton exchange membrane fuel cell (PEMFC) with porosity is investigated in this study using a two-phase, half-cell model. The thin film agglomerate approach is used to model the catalyst layer. Both vapor transport and liquid water transport in the PEMFC are examined in this study. Proton transport is much faster than the gaseous and liquid water transport. The ionic potential reaches a steady state level in ∼10 −1 s but liquid water transport takes ∼10 s. The variation of the ionic potential loss reaches a critical value, decreasing to a steady state, and is not monotonic. The gas diffusion layer (GDL) and the catalyst layer (CL) porosity, which can affect cell performance, have been carefully investigated. The current density rises rapidly within 10 −2 s, then remaining constant. After 1 s, this is affected by the cell voltage, GDL porosity, and CL porosity, and if the GDL porosity is below 0.4, the current density drops. For the gas diffusion layer porosity, the current density increases between ɛ GDL = 0.2 and ɛ GDL = 0.5, with increased GDL porosity. For the catalyst layer porosity, the optimum value appears between ɛ CL = 0.06 and ɛ CL = 0.1.