Methods of estimating frequency skew in a packet network include determining a representation of a packet delay variation (PDV) sequence from an initial estimate of frequency skew between master and slave devices in the packet network and timestamps transmitted therebetween. An operation is performed to extract a statistical mode from an empirical probability distribution function (PDF) of the representation of the PDV sequence, where the statistical mode corresponds to a value at which the PDF has its maximum value. The, an updated estimate of the frequency skew is generated by determining a slope between timestamps at indices associated with a plurality of points in the representation of the PDV sequence that are within a range of the statistical mode.