Fuel cells are one of the zero-emission elements of modern automotive drive systems. This article presents theoretical identification of the component parameters of indicators for the fuel cell operating conditions. Activation, ohmic, and mass transport losses were identified. Current–voltage characteristics were provided along with an analysis of typical cell losses. The actual performance characteristics of fuel cells were analyzed for Toyota Mirai I and II generation vehicles. The fuel cells operating conditions were derived and analyzed in the context of real driving conditions. Therefore, urban, rural, and motorway conditions were used. The vehicles were equipped with PEM fuel cells supplying power equal to 114 kW (1st gen.) or 128 kW (2nd gen.). The average fuel cell stack power values depend on the driving conditions: urban (about 10 kW), rural (20 kW) and motorway (about 30–40 kW) driving modes. The different power ratings of fuel cells combined with different battery generations resulted in a variation in the cells operating conditions. Analyses conducted in various traffic conditions indicated the possibility of determining losses related to the fuel cells. The analysis of fuel cell losses shows the greatest values for activation losses when the cells are under high load (for both generations)—i.e., in motorway driving conditions. The voltage of resistive losses reached its maximum in urban driving conditions when the load on the fuel cells was small.