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© 2023 IEEE. Personal use is permitted, but republication/redistribution requires IEEE permission., In this paper, a fuel cell system supervisory controller is developed for a fuel cell-based hybrid electric vehicle to safely control the interactions between powertrain components, maximize efficiency and minimize the degradation of the fuel cell. The proposed fuel cell supervisory controller includes three main elements: a state machine, an optimal setpoint generator and a power limit calculator. The state machine, as the top layer of the supervisory controller, is responsible for coordinating the various subsystems of the fuel cell, including the three subsystems, anode, cathode, thermal, and the DC/DC converter. The primary purpose of the state machine is to ensure global control over these subsystems as well as facilitate communication between the fuel cell system, diagnosis system, and Vehicle Control Unit (VCU). The state machine not only allows for the appropriate transitions between states but also governs the fuel cell system operation in all its different operating states such as Start-up, Shutdown and Run. The optimal setpoint generator is responsible for determining the operating conditions of the fuel cell system that maximizes the system's efficiency. It is designed by taking into account the comprehensive model of the fuel cell stack, considering manufacturing constraints, and incorporating the compressor map which then provides the optimal setpoints for all the subsystems' local controllers. A power limit calculator is also developed to compute the stack available power and feeds this information to the energy management system in the VCU. This information is used by the VCU to split the requested power between the fuel cell and the battery. The experimentally validated stack model and the complex model of the subsystems based on the Inn-Balance project data are used in the simulation. Furthermore, the subsystems' local controllers used in the MATLAB-Simulink were validated in a real vehicle test bench. The Common Artemis 130 km/h Driving Cycle (CAD, This work was supported in part by the Spanish State Research Agency through the Maria de Maeztu Seal of Excellence to IRI (MDM-2016-0656), and and in part by the Fuel Cells and Hydrogen 2 Joint Undertaking under Grant INN-BALANCE 735969. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and Hydrogen Europe and N.ERGHY . Finally, the work acknowledges the support of the MAFALDA project funded by the Spanish Ministry of Science and Innovation (PID2021-126001OB-C31)., Peer Reviewed, Postprint (author's final draft)