The increasing need for power conversion systems that are efficient and reliable in fuel cell systems has created the demand for advanced control methods to maximise the performance of power electronic converters. The efficiency of an interleaved boost converter (IBC) controlled by a conventional Proportional-Integral-Derivative (PID) controller and by a fuzzy logic controller (FLC) when used in fuel cell applications is compared here. Fuel cell systems leverage the benefits of topology in the IBC, including decreased input current ripple, increased efficiency, and enhanced power density. To solve the nonlinearities and uncertainties inherent in fuel cell dynamics, the FLC provides greater robustness and flexibility in terms of handling non–linearity and steady state error over the PID controller, which is the most used due to its simplicity and effectiveness. Dynamic response, efficiency, robustness to varying load conditions and changes in input voltage, and output voltage regulation are some of the performance parameters simulated with MATLAB/Simulink. From the simulation, the FLC-based IBC operations are superior to the PID-regulated IBC with lower overshoot, quicker transient response, and better disturbance rejection. This renders it more suitable for fuel cell operations where efficiency and operation stability are paramount. The results of this work, as described below, present useful guidelines on the design and selection of control schemes for guaranteeing maximum power converter efficiency in fuel cell-based battery charging systems.