This article deals with implementing a rule-based control method and startup sequence of a hybrid electric vehicle powered by a modular fuel cell system as its primary energy source and a lithium-ion battery system as its secondary energy source. The modular fuel cell system is composed of two separate fuel cell systems, electrically coupled to a one-power converter, using a programmable device. Depending on the vehicle’s operating mode, either both systems are used or just one of them. The vehicle’s fuel efficiency is improved by operating at constant power in the peak efficiency range of each fuel cell system. The experimental results show that the proposed system can significantly improve the fuel economy of a fuel cell vehicle and extend the driving range, while avoiding start/stop cycles. Additionally, this solution can increase the fuel cells’ lifecycle.