Global climate change, energy independence and sustainability have encouraged automotive sector stakeholders to adopt further technological researches on the integration of Fuel Cell (FC) within Electric Vehicles (EVs). This paper aims at presenting a multi-stack FC configuration inside the EV to minimize its start up, heating/cooling, and cycling problems via proposing a novel thermal management approach. Simulation results, using MTCSim© software, illustrates that proper thermal management of the EV’s multi-stack FC significantly enhances its life span, cycling, and efficiency, besides optimizing its operation performance.