Three different activation procedures of phosphoric acid-doped polymer fuel cells have been analyzed: a discontinuous procedure with daily startup and shutdown, a continuous procedure without interruption and a continuous procedure after 1 h of direct exposure of the MEA to the atmosphere. The investigation was carried out analyzing the voltage profiles over time, the high frequency impedance and complete impedance spectra. The results show that the voltage increase during activation is due to the reduction of the kinetic resistance. The continuous activation leads to the best performance (0.678 V in 100 h) while the discontinuous one leads to a lower performance in a shorter time (0.665 V in 50 h). The initial exposure of the MEA to the atmosphere alters the initial acid distribution and leads to a final performance of (0.664 V in 200 h) in spite of the continuous activation.