Hydrogen is a promising energy carrier to allow the reach of the zero-emission targets established for the next years. Polymeric Electrolyte Membrane FC are studied inside the HI-SEA laboratory of the University of Genoa, to assess the opportunities of this technology on marine applications. Here, 8 PEMFC stacks, sized 30 kW each for a total power installation of 240 kW, have been tested to draw guidelines for the best system design onboard ships and to deepen the know-how on the experimental management of the technology. During the tests, it was possible to observe the reciprocal influence of some parameters, which may influence the system efficiency. In this work, a statistical investigation is developed to quantify the cell voltage variation correlated to the values of temperature and current. This has been possible thanks to Design Expert (DE), a software developed by Stat-EASE, Inc. Through the Design of Experiment approach, it is possible to evaluate the significance of variables in the FC system, called factors. The experiment under consideration is also characterized by non-controllable factors, cause of disturbances that induce further variability in the response. Eventually, it was possible to analyse the significance of the parameters involved, to build a regression model by performing the analysis of variance with which the significant values are identified, and to assess the presence of outliers.