Water and proton dynamics in an functioning proton exchange membrane fuel cell (PEMFC) were probed with quasi-elastic neutron scattering (QENS). By operating the specially designed neutron-transparent fuel cell in a “proton pump” mode, we were able to perfectly control the membrane hydration, which allowed us to discriminate the impact of electric field on water molecules diffusivity from pure hydration effects. By cross-analyzing the fuel cell QENS spectra taken over extended range of time scales, we demonstrate that protons exhibit the same dynamical behavior as in an ex-situ membrane at the same level of hydration, e.g., slow hopping motions of adsorbed protons (mostly H3O+) and subdiffusive confined motions of hydration protons (H2O). These mechanisms are maintained on applying a current up to 0.1 A/cm2. With this work, we establish the applicability of QENS to monitor in situ the molecular dynamics in PEMFC, and prove that knowledge extracted from ex situ proton conducting electrolytes can be transposed to the full operando cells.