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The non-linear behavior of the voltage-current (V-I) fuel cells' output curve is one of the major issues the scientific community deals with, in order to improve fuel cell technology and expand its use to both domestic and industrial applications. Many power conditioning topologies of a fuel cell's output electrical energy have been presented in the past years, but the DC/DC interleaved boost converter (IBC) topology seems to be one of the most attractive solutions. Therefore, IBC control schemes become a key factor in fuel cell energy systems and the use of embedded systems is highly indicated for efficient and reliable real-time control. The traditional methods of programming microcontrollers via ldquoCrdquo or Assembly language, may take a respectable amount of time to develop, significantly slowing down the procedures for system development and validation. This paper presents a new model-based rapid prototyping method for programming embedded systems using Matlab/Simulinkreg models. The embedded control system (ECS) is designed to control the input current of an IBC connected to a fuel cell, by suitably varying the switching signals which drive the power switches on the IBC.