In this paper, parallel operation systems with Z-source Inverters for the fuel cell systems are discussed. The carrier phase shifted SPWM(Sinusoidal Pulse Width Modulation) has an advantage in reducing harmonics of output current. However when this technique applies in parallel operation of Z-source inverters, it additionally produces circulating currents. The circulating current is analyzed and a method to prevent the circulating current is applied to the parallel operation systems of Z-source inverters. To maintain high performance with reduced circulating current in inverter output and low harmonic components in load current, circulating current reactors are used. The proposed approach is verified through simulation and experiment.