Hydrogen Fuel Cell Vehicle(HFCV) is system that uses electrical energy of fuel cell stack to main power source, which is different system with other vehicles that use high-voltage, large-current. Isolation performance of this system which is connected with electrical fire and electrical shock is important point. Isolation resistance of electric installation is divided according to working voltage, it follows criterion more than $100{Omega}$/VDC (or $500{Omega}$/VAC) about system operation voltage in a hydrogen fuel cell vehicle. Although measurement of isolation resistance in a hydrogen fuel cell vehicle is two methods, it uses mainly measurement by megger. However, the present isolation resistance measurement system that is optimized to use in electrical facilities is unsuitable for isolation performance estimation of a hydrogen fuel cell vehicle because of limit of maximum short current and difference of measurement resolution. Therefore, this research developed the isolation resistance measurement system so that may be suitable in isolation performance estimation of a hydrogen fuel cell vehicle, verified isolation performance about known resistance by performance verification of laboratory level about developed system, and executed performance verification through comparing results of developed system by performance verification of vehicle level with ones of existing megger. Developed system is judged to aid estimation and upgrade of isolation performance in a hydrogen fuel cell vehicle hereafter.