To achieve a good performance, proton exchange membrane fuel cells (PEMFCs) require a delicate water balance through the design of cells and selection of operating conditions. In this study, the impact of ionomers with different side-chain lengths, having different water retention capability, serving as binder in the catalyst layers is investigated experimentally for both catalyst layer structure and the resulting cell performance under a wide range of reactant flows and cell operating pressures. The results show that cells with the short side-chain (SSC) ionomers, having a higher water retention capability, achieve a higher cell performance, active surface area, platinum utilization, and porosity than the cells made by the conventional long side-chain (LSC) even under fully humidified condition, in contrast with studies reported in literature. This is achieved for the high reactant flow, which has a higher water removal capability. The SSC ionomer with the low equivalent weight of 720 results in a significantly higher cell performance with the maximum power density of 1.3 W/cm(2) at the high reactant flow. SSC with the equivalent weight of 790 has a good balance between water retention and water removal in the catalyst layer at a lower airflow. The performance of the cells with the SSCs is better, and it is far less sensitive than, the cells with the LSC when the operating pressure is increased.