Described is a low latency re-timer for systems supporting spread spectrum clocking. The re-timer comprises: a first clock frequency estimator to estimate a frequency of a receive clock (RX CLK) and to provide a first timestamp associated with a first clock that underwent spread spectrum; a second clock frequency estimator to estimate a frequency of a transmit clock (TX CLK) and to provide a second timestamp associated with a second clock that underwent spread spectrum; and a comparator to compare the first timestamp with the second timestamp.