This paper presents a nonlinear model-based control for multiphase interleaved boost converter used in fuel cell applications. This control scheme is based on the differential flatness concept, which generates the reference trajectories to characterize the dynamics and solve the inverse dynamic problems. A prototype of a fuel cell converter was constructed in the laboratory to validate the proposed technique. The implementation of the control algorithm was done by connecting the prototype with a dSPACE DS1202 MicroLabBox interfacing card. The control scheme demonstrated excellent experimental results for use with a 2.5-kW polymer electrolyte membrane fuel cell (PEMFC) on the subject of the steady state and dynamic behaviors along with the control robustness.