A method was developed to improve the measurement accuracy of track circuit frequency shift keying (FSK) signal by using FPGA and ARM processor. The quantization timer was used to measure the periods of FSK signal in FPGA, and then data was translated to ARM after temporarily stored in dual-port RAM. The ARM processor analyzed the period of the high frequency carrier signal and the main reasons for causing FSK error, and compensated the distortion data which caused by switching of up frequency and down frequency. The results show that this system can precisely measure the low frequency modulation and high frequency carrier signal frequency, and it can satisfy the requirement of speed and precision in industry environment.