A system for measuring the insulation resistance of a fuel cell vehicle is provided. The system includes a fuel cell that supplies power, a rechargeable high-voltage battery, and a bidirectional converter, disposed between an output terminal of the fuel cell and the high-voltage battery, to adjust a voltage at the output terminal of the fuel cell. A fast measurement unit measures the insulation resistance of the fuel cell vehicle by being connected to the output terminal of the fuel cell and a second measurement unit measures the insulation resistance of the fuel cell vehicle by being connected to the output terminal of the high-voltage battery. A controller operates the bidirectional converter based on the state of the fuel cell vehicle and measure the insulation resistance of the fuel cell vehicle using the first measurement unit or the second measurement unit