The present invention relates to a system and method for controlling power distribution of a fuel cell hybrid electric vehicle. The system includes a fuel cell, a battery, a DC/DC converter connected to the battery for the input and output of power, an inverter connected to the DC/DC converter and fuel cell, a motor connected to the inverter, and a controller for estimating the required vehicle power. Further the present invention controls power transmission between the fuel cell, the battery, the DC/DC converter, and the inverter. The controller selectively performs control into one of a fuel cell mode, a battery discharge mode, a battery charge mode, and a regeneration mode.