Performance of individual cells in an operating polymer electrolyte membrane (PEM) fuel cell stack is different from each other because of inherent manufacturing tolerances of the cell components and unequal operating conditions for the individual cells. In this paper, first, effects of different operating conditions on performance of the individual cells in a two-cell PEM fuel cell stack have been experimentally investigated. The results of the experiments showed the presence of a voltage difference between the two cells that cannot be manipulated by operating conditions. The temperature of the supplying air among others predominantly influences the individual cell voltages. In addition, those effects are explored by using a dynamic model of a stack that has been developed. The model uses electrochemical voltage equations, dynamic water balance in the membrane, energy balance, and diffusion in the gas diffusion layer, reflecting a two-phase phenomenon of water. Major design parameters and an operating condition by conveying simulations have been changed to analyze sensitivity of the parameters on the performance, which is then compared with experimental results. It turns out that proton conductivity of the membrane in cells among others is the most influential parameter on the performance, which is fairly in line with the reading from the experimental results.