An apparatus and method for clock regeneration with low jitter. The method includes the following steps: (a) using a phase lock loop to generate a first clock that is phase locked to a reference clock; (b) using a binary phase detector for generating a phase error signal by detecting a timing difference between the input signal and a second clock; (c) filtering the phase error signal to generate a first control word and a second control word; (d) performing a phase rotation on the first clock by an amount controlled by the first control word to generate the second clock; (e) filtering the second control word to generate a third control word; (f) sampling the third control word to generate a fourth control word using a third clock; and (g) performing a phase rotation on the first clock by an amount controlled by the fourth control word to generate the third clock. Comparable features for performing these steps are provided in the apparatus.