Abstract: The method for running in a fuel cell of the PEMFC type includes at least a first running-in phase, then an operation of reversing the direction of the hydrogen and air flows, then a second running-in phase. The running-in phases each includes a fuel cell stabilisation step in which the current density produced by the cell is kept constant at a low value for a given period, then an oxygen depletion step, during which the current density is kept constant at a minimum value, less than or equal to the low value, and during which the air supply is at least partially cut off, being adjusted so as to obtain a cathodic stoichiometric coefficient strictly less than 1. The oxygen depletion steps of the first and second run-in phases end when the cell voltage of the fuel cell reaches a predefined threshold voltage.