In this paper, the characteristics of portable fuel cell system are introduced and the dynamic response of output voltage of fuel cell stack with internal humidifier is analyzed. When the output of the fuel cell (FC) stack is short-circuited for humidification, the output voltage of the FC stack rapidly drops. In order to maintain the load voltage in the required range, dynamic compensation methods are proposed: 1) installing a capacitor behind the output of the FC stack; 2) utilizing the bi-directional converter. Especially, bi-directional converter is used when short of the FC output is detected or predicted by algorithm using data which is measured during previous three cycles. These methods are simulated by PSIM 9.0, then experimental results from the fuel cell system prototype verify the validity of the proposed methods.