A three-dimensional transient two-phase isothermal model has been developed for the cathode side of a proton exchange membrane fuel cell (PEMFC). This has been done in order to fully investigate the effects and the time variation of liquid water formation as well as the gas phase transport under the start up condition. It is considered that the generated water in the cathode catalyst layer (CL) is liquid water and that the gas diffusion layer (GDL) is hydrophobic. A non-equilibrium water condensation-evaporation is also assumed. The time variations of liquid water distribution in along-channel and through-plane directions are investigated. This is to determine the liquid water accumulation at the start up time (above the channel under the CL), then the movement of the liquid water in the domain and the final accumulation at the steady state condition (above the rib and near the CL). It has also been found that it takes less time for a high average current density to attain the steady state condition which is due to the capillary pressure gradient inside the porous media. Validation of the numerical results has been implemented via a polarization curve comparison with the experimental data. Both sets show good agreement.