Fuel cell (FC) stacks are modular low voltage in nature and are used in high power and higher voltage applications. During the operation, the power from stacks varies dynamically with variations in different operating parameters resulting in mismatch in their electrical performance. If a large number of FC stacks are directly connected in series to achieve higher voltage and even if one of the series connected stacks is under performing, the current from the entire branch gets affected leading to reduced power. This paper proposes a scheme to extract maximum power from an FC stack array by using a dedicated power converter (DPC) across each FC stack along with a maximum power point tracking (MPPT) controller. However, operating the underperforming FC stacks at MPP may further degrade its performance. Hence, they are proposed to be operated at maximum fuel efficiency point (MFEP) instead of MPP. Tracking the MFEP ensures economy of reactant gases and safe operating voltage levels for the underperforming stacks. Phase shifted converters are used as DPCs for better conversion efficiency. The efficacy of the scheme is analyzed using Simulink and validated with experimental results.