A jitter compensation system in a rotary recording medium reproducing apparatus having a reproducing transducer including a reproducing element for reproducing recorded signals from a rotary medium, where the rotary recording medium is recorded with an information signal and also recorded with reference signals for tracking control with predetermined periods, comprises a separation circuit for separating the reference signals from a signal reproduced by the reproducing transducer, a detection circuit for detecting the separated reference signals and obtaining a signal having a predetermined period and predetermined frequency, a standard signal supplying circuit for supplying a standard signal having a frequency equal to the predetermined frequency, a phase comparator for comparing phases of the predetermined frequency signal thus obtained and the standard signal supplied thereto, to produce a phase comparison error signal, and a displacing circuit for displacing the reproducing element of the reproducing transducer along a relative scanning direction with respect to the rotary recording medium, in response to the output error signal of the phase comparing means.