Optical fiber time delay system has been widely used in optical-controlled phased array antenna, radar distributed network, interferometric optical fiber hydrophone and high-speed photoelectric chip. These applications require high-accuracy and high-stability time delay generated by the system. Time delay measurement directly determines the precision and resolution of the system. Therefore, high-precision time delay measurement method is of great significance in developing the optical fiber delay system. In this paper, progress and problems of optical fiber time delay measurements are discussed. A new method of precisely measuring the time delay in optical fiber is proposed. We use the frequency domain reflectometry (FDR) to avoid the discrepancy between measuring range and measuring precision, which exists in both time-of-flight (TOF) method and phase discrimination approach. An intensity modulated 1064 nm laser signal is used as a light source. The modulation frequency is tuned from 10 MHz to 200 MHz in steps of 0.5 MHz. The spectrum of echo signal is obtained by measuring the amplitudes and phases of echo signals at different frequency points. The delay information is obtained via the inverse fast Fourier transform (IFFT). The precision of delay measurement in our method is determined by step size of frequency variation, and a higher-precision measurement is realized by using interpolation zero algorithm. Since our method is not to modulate the optical frequency, but to control the frequency of the modulation signal loaded on the electro-optic modulator, it is easy to achieve the high-precision and high-linearity frequency modulation. In this paper, theoretical analysis and time delay measurement are used to compare the FDR method with conventional TOF measurement method. The accurate measurement of 33–200 ps is realized, and measurement error is lower than 7 ps. We also design an incremental measurement experiment to study the resolution of the FDR method, which achieves a delay resolution of 3.3 ps. The influence of temperature jitter is analyzed to prove the reliability of experimental results. It proves that the FDR method has a higher measuring accuracy than the TOF method. The time delay measurement precision can be further improved by expanding the modulation bandwidth. Our method is to be applied to an optical fiber delay system to improve the precision and resolution of system delay.