This research proposes an improved energy management strategy (EMS) for a fuel cell hybrid power system for an electric aircraft based on a recently developed coyote optimization algorithm (COA). The suggested hybrid system consists of fuel cells and an energy storage system (ESS) to supply the required load in stable conditions. The distribution and performance of the hybrid electrical power system are determined by various energy sources. Consequently, having the best energy management system is essential for completing this work. The suggested EMS’s main objectives are to reduce hydrogen energy utilization and increase power source longevity. The proposed coyote optimization algorithm with external energy maximization strategy (COA-EEMS) and coyote optimization algorithm with equivalent consumption minimisation strategy (COA-ECMS) are tested with the help of the Opal-RT 5700 real-time HIL simulator and MATLAB/Simulink. The proposed algorithms confirm their robustness and higher efficiency by minimizing hydrogen fuel consumption compared to existing algorithms. The merits of the proposed algorithms are presented in detailed and compared with existing algorithms.