A pore-scale description of species and charge transport through a bilayer cathode catalyst layer (CL) of a polymer electrolyte fuel cell using a direct numerical simulation (DNS) model is presented. Two realizations of the bilayer catalyst layer structure are generated using a stochastic reconstruction technique with varied electrolyte and void phase volume fractions. The DNS calculations predict that a higher electrolyte phase volume fraction near the membrane-CL interface provides an extended active reaction zone and exhibits enhanced performance. A higher void phase fraction near the gas diffusion layer aids in better oxygen transport. The effects of cell operating conditions in terms of low inlet relative humidity and elevated cell operating temperature on the bilayer CL performance are also investigated. Low humidity and elevated temperature operations exhibit overall poorer performance compared to the high humidity and the low-temperature operations, respectively.