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Digital control implementation is crucial in modern power electronic converters and energy conversion systems, as more complex control and friendly user interface are required. The fuel cell (FC) is a promising clean energy source and a reliable technology for niche applications providing high conversion efficiency. In this paper, a digitally controlled FC system is documented based on the boost-inverter topology that achieves both boosting and inversion functions in a single-stage. A digital signal processor TMS320F28335 is used to implement the control of the FC system in order to provide a number of benefits including low-cost, good performance, an easy implementation of a relatively complicated algorithm, and user friendly interface. The control design, analysis, simulation and experimental results are presented in the paper to confirm the performance of the digitally controlled FC system.