Ejector-based proton exchange membrane fuel cells (PEMFCs) are of great interest due to their simplicity and feasibility. Thus, proton exchange membrane fuel cells are considered the most suitable technology for in-vehicle systems, industrial applications, etc. Despite the passive characteristics of the ejector, active control of the hydrogen supply system is needed to ensure sufficient hydrogen, maintain the stack pressure, and ensure effective entrainment. In this research, a novel semi-empirical model is proposed to accurately predict the entrainment performance of the ejector with an 80 kW fuel cell system. According to the precise semi-empirical model, the hydrogen supply system and the anode channel are modeled. Then, a fuzzy logic controller (FLC) is developed to supply sufficient and adequate gas flow and maintain the rapid dynamic response. Compared to the conventional proportional–integral–derivative controller, the fuzzy logic controller could reduce the anode pressure variability by 5% during a stepped case and 2% during a dynamic case.