A fuel cell system and a method for controlling the same corrects concentration sensing values by estimating temperature according to the load amount of a stack. A control method of a fuel cell system including the steps of: measuring the load amount of loads supplied with power from a stack; estimating temperatures at the area where a concentration sensor is installed from the load amount values; producing the corrected concentrations by correcting the concentration sensing values according to the estimated temperatures; and controlling the drive of the fuel cell system according to the corrected concentrations.