An apparatus and a method for measuring the internal ohmic resistance of a fuel cell system, in which the resistance can be easily measured through a current interruption method even while the fuel cell system is operated. An interrupter and an external energy consumption device are connected in parallel to each other between a fuel cell and a main energy consumption device such that current to the external energy consumption device is applied and interrupted by switching the interrupter on/off even while the fuel cell system is maintained in operation as is, thereby making it possible to easily measure the internal ohmic resistance of the fuel cell.