Real-time frequency measurement for non-repetitive and statistically rare signals are challenging problems in the electronic measurement area, which places high demands on the bandwidth, sampling rate, data processing and transmission capabilities of the measurement system. The time-stretching sampling system overcomes the bandwidth limitation and sampling rate limitation of electronic digitizers, allowing continuous ultra-high-speed acquisition at refresh rates of billions of frames per second. However, processing the high sampling rate signals of hundreds of GHz is an extremely challenging task, which becomes the bottleneck of the real-time analysis for non-stationary signals. In this work, a real-time frequency measurement system is designed based on a parallel pipelined FFT structure. Tens of FFT channels are pipelined to process the incoming high sampling rate signals in sequence, and a simplified parabola fitting algorithm is implemented in the FFT channel to improve the frequency precision. The frequency results of these FFT channels are reorganized and finally uploaded to an industrial personal computer for visualization and offline data mining. A real-time transmission datapath is designed to provide a high throughput rate transmission, ensuring the frequency results are uploaded without interruption. Several experiments are performed to evaluate the designed real-time frequency measurement system, the input signal has a bandwidth of 4 GHz, and the repetition rate of frames is 22 MHz. Experimental results show that the frequency of the signal can be measured at a high sampling rate of 20 GSPS, and the frequency precision is better than 1 MHz.