An apparatus and method for synchronizing sampling frequencies of a receiver and a transmitter of a multi-carrier communication system is provided. The receiver includes an estimator for estimating a frequency offset by employing an additional angle rotation of a received signal in frequency domain. The apparatus includes a compensation loop filter for generating a first output in response to a frequency offset compensation, an adder for adding the estimated frequency offset and the first output to generate a second output, and a loop filter for generating frequency offset compensation according to the second output. The method repeatedly applies the apparatus to generate frequency offset compensation, and then feeds it back to an oscillator to compensate the sampling frequency of the receiver. The apparatus and method can also be applied to a communication system with a carrier frequency offset.