This paper presents that generation and propagation mechanism of low frequency current ripples generated by a rectification effect of an inverter in fuel cell generation system is analyzed. The ripple reduction methode using hardware components such as capacitors and inductors is examined to reduce low frequency current ripples. A new fast and robust low frequency current ripple elimination algorithm is then proposed to incorporate a single loop current controller, which directly controls fuel cell current, without any extra hardware. The proposed algorithm can completely eliminate this current ripple as well as an overshoot or undershoot is significantly reduced. And the de link voltage and output current are well regulated by inverter controller. The validity of proposed algorithm is verified both computer simulation using PSIM 6.0 and experiment with a 1kW laboratory prototype.