Provided are a synchronizing apparatus and method for performing synchronization in a packet network. The synchronizing apparatus includes a sampling unit to measure a time difference using a plurality of time stamps included in a plurality of two-way message packets, an estimating unit to estimate a frequency offset by applying a baseline algorithm to the time difference, a verifying unit to verify the frequency offset to remove an error caused by network delay variation, and a synchronizing unit to remove the frequency offset from a local slave clock signal and generate a slave clock signal synchronized to a clock signal of a master device.