Methods and apparatus are provided for digital compensation of clock timing errors in a VCDL. Clock timing errors in a clock and data recovery system having a voltage controlled delay loop comprised of a plurality of delay elements are compensated for by evaluating a phase of data recovered from an input signal; generating one or more uncompensated clock phase adjustment values based on the phase evaluation; generating one or more compensation terms that compensate for a non-ideal delay for one or more of the delay elements; and determining an adjustment to one or more clock phases produced by the voltage controlled delay loop based on the uncompensated clock phase adjustment values and the one or more compensation terms. The one or more compensation terms can be subtracted from the uncompensated clock phase adjustment values to generate the adjustment to the one or more clock phases.