A power controlling apparatus for a fuel cell system includes a fuel cell controller which analyzes power state information of a fuel cell system, transmits a power state information signal based on the analysis to a power conversion controller, receives a load request power information signal from the power conversion controller, analyzes the received load request power information signal, and changes an outputtable power amount based on the analysis. The power controlling apparatus also includes a power conversion controller which transmits a load request power information signal based on power information requested by a load to the fuel cell controller, analyzes the power state information signal transmitted by the fuel cell controller, and controls a power convert amount based on the analysis.