In general, fuel cells generate high-current low-voltage unregulated electricity in the form of direct current, which is not suitable for electrical appliances due to its low voltage. Therefore, a high-power boost converter is required for adjusting the output voltage from fuel cells to the desired level in order to distribute high-voltage power at a constant rate. In this study, a parallel multiphase step-up power circuits with an interleaving method was used to increase voltage and distribute electric currents in many phases to reduce the current rating of the switching device in each phase. Meanwhile, an interleaving technique was employed for shifting phases of electric currents in order to reduce the sum of ripple currents in fuel cells in response to the nonlinear behaviors of the switching circuit. This article presents a nonlinear model-based control approach based on the differential flatness method for the interleaved boost circuits used in fuel cell applications. The fuel cell converter was connected to dSPACE DS1202 MicroLabBox, as well as inspected and implemented by a polymer electrolyte membrane fuel cells (PEMFC, size 2.5 kW) in terms of steady state, dynamic characteristics, and control robustness. The findings from this study were very satisfactory, and when experimentally compared with the classical proportional–integral (PI) control scheme, it was found that the differential flatness control could better respond to load changes.