Methods for improving the accuracy of reference frequency and time signals transmission using a new fiber-optic modem with phase instability compensation are presented. Algorithms for transmitting a 1PPS pulse time signal with a synchronization error of no more than 200 ps are considered. The results of measurements of the Allan deviation during the transmission of a reference signal with a frequency of 100 MHz through a two-kilometer fiber-optic line with additional external temperature impact are presented. With the help of the developed fiber-optic line emulator, the accuracy of reference signals transmission for fiber lines up to 100 km long, as well as for various external impacts, has been estimated. A full-function device for transmitting and receiving reference frequency and time signals through a fiber-optic communication line up to 100 km long, the instability characteristics of which reach approximately 1–3·10–17 in the daily measurement interval, has been developed.