Transients have utmost importance in the lifetime and performance degradation of PEM fuel cells. Recent studies show that cyclic transients can induce hygro-thermal fatigue. In particular, the amount of water in the membrane varies significantly during transients, and determines the ionic conductivity and the structural properties of the membrane. In this work, we present three-dimensional time-dependent simulations and analysis of the transport in PEM fuel cells. U-sections of anode and cathode serpentine flow channels, anode and cathode gas diffusion layers, and the membrane sandwiched between them are modeled using incompressible Navier-Stokes equations in the gas flow channels, Maxwell-Stefan equations in the channels and gas diffusion layers, advection-diffusion-type equation for water transport in the membrane and Ohm’s law for ionic currents in the membrane and electric currents in gas diffusion electrodes. Transient responses to step changes in load, pressure and the relative humidity of the cathode are obtained from simulations, which are conducted by means of a third party finite-element package, COMSOL.