Effective water management is necessary to prevent the performance degradation of polymer electrolyte membrane fuel cells (PEMFCs). In this study, acoustic pressure waves (AWs) are superimposed on an oxygen gas flow passing through a cathode to evaluate its potential to mitigate the flooding issue in flow channels. The goal is to expedite droplet removal by exciting droplets at frequencies close to their natural frequency. In-situ experiments are conducted to investigate the influence of AWs on two-phase flows in the cathode channel and the corresponding PEMFC performance. When AWs are applied, the frequency of water discharge from the cathode channel increases, and reduces the internal accumulated water, resulting in the pressure drop decreases. The internal flooding is also decreased, resulting in the reduction of the high frequency resistance attributed to decreased contact resistance. The external excitation improves the PEMFC performance owing to the effective and frequent water discharge induced by the increase in the local inertial force related to the droplet oscillation. The water management method propose in this study is considered to be an efficient method not only for PEMFC systems but also for other systems requiring water management.