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Fuel cell power systems have increasingly become popular because of their inherent advantages over conventional energy systems. A fuel cell system typically requires some kind of power conditioning that usually includes a DC-DC converter and a DC-AC inverter. In a single phase system, the operation of a single phase inverter introduces a second harmonic (120 Hz) current ripple into the system. This ripple has been found to be detrimental to the performance, life and efficiency of the fuel cell if it is not adequately controlled. This paper proposes an active filtering method to cancel the second harmonic current ripple drawn from the fuel cell source in a single phase fuel cell system. This approach provides an alternate path for the 120 Hz current preventing it from flowing through the fuel cell. The conventional and the proposed systems have been simulated using PSpice and the results have been presented. Experimental results from a laboratory prototype are also included to validate the proposed approach. A major feature of this implementation is the use of a DSP TMS 320F2808 for the overall control and monitoring of the system.