An all-fiber Faraday rotator isolation rate measurement system is designed and realized. The system has tremendous advantage for large aperture Faraday isolator on-line measurement due to its flexible alignment and more compaction. Employing the method of relative transmission measurement and transmissions contrasting between static and operating states, single-shot isolation-rate measurement is achieved. The available measurement range larger than 33 dB is demonstrated experimentally. And the potential to get measurement range larger than 50 dB by adjusting the coupling rate of the fiber couplers is affirmed. Measurement accuracy of 2.2%of PV value is achieved even while keeping the input pulse energy and polarization in random vibration, which illustrates that the influence of the input pulse energy and polarization vibration on the measurement accuracy is eliminated.