An apparatus and method for transmitting/receiving an S-SCH in an Institute of Electrical and Electronics Engineers (IEEE) 802.16m wireless communication system are provided. A method for transmitting, by a transmitter, a Secondary Synchronization CHannel (S-SCH) in a communication system includes generating a sequence depending on a cell IDentification (ID), determining a subcarrier set comprising subcarriers to map the generated sequence, based on a Fast Fourier Transform (FFT) size and a segment ID, and mapping the generated sequence to the subcarriers of the determined subcarrier set.