When input parameters like gas volume or load of the fuel cell system is changed, the fuel cell system can generate transient voltage disturbances. In this paper, a fuel cell system with Z-source inverter and ultracapacitors for voltage disturbance compensation is proposed. The structure of Z-source inverter is simple. It has unique features that can boost/buck input voltage with a DC/DC converter using only a modified switching pattern. The characteristics of the proposed topologies for the fuel cell system with Z-source inverter and ultracapacitors are analyzed using simulation, and verified by experiments. The simulation and experimental results show that the proposed system is capable of operating with stable response to the system transient and voltage disturbances.