This paper deals with on-board energy management of hybrid fuel cell vehicles equipped with a polymer electrolyte membrane fuel cell (FC) stack and a battery pack as main power source and hybridizing device, respectively. A multilevel architecture was conceived to separately manage on-board energy flows and mutual interaction between FC auxiliaries and powertrain components. At the highest-level, a splitting index map was designed to share the power requested by the driver among the fuel cell stack and batteries as function of traction power demand and batteries’ state of charge. At the intermediate-level are defined the set points at which to operate the fuel cell system (FCS) to achieve maximum efficiency. Then, at the low-level, specific control strategies are adopted to reach the set point as addressed by the intermediate-level. To guarantee the accuracy required for control strategy development, a mixed modeling approach was followed to simulate vehicle powertrain, FCS, electrochemistry, and water management. The simulations were carried out for a 60 kW FC powertrain running under severe transient maneuvers. The results show the potentialities of the proposed approach for energy management optimization, control, and diagnostics analyses.