A novel technique to perform ultra-wideband instantaneous frequency measurement in real-time based on differential photonic time-stretch is proposed and experimentally demonstrated. Wideband frequency measurement is enabled by time-stretching the RF input signal via the dispersion compensating fiber. Distortion of the measured frequency signal caused by the non-uniformity of the spectrum of the pulsed laser source, which can be found in most of traditional time-stretch systems, is eliminated here by implementing a dual-output Mach–Zehnder modulator (DOMZM) with complementary outputs and a balanced photodetector. Multi-tone tests with a 20 GHz frequency measurement range are conducted to verify the feasibility of the system of measuring multiple frequency signals. Followed by the proposed automated digital signal processing algorithms, our instantaneous frequency measurement system offers an ultra-fast sweep time of 10 ns, a frequency resolution of 660 MHz, and a measurement error within ±380 MHz. A larger frequency measurement range can be realized by implementing a DOMZM with a larger bandwidth.