A method of a mobile station for transmitting a ranging signal in a wireless communication system which supports Fractional Frequency Reuse (FFR) and an apparatus for performing the method are provided. The method includes receiving information of ranging resource allocation, from a base station, based on the information of the ranging resource allocation, determining a cell identifier and a Frequency Partition (FP) location for uplink control channels, determining a subband index for the ranging resource allocation based on the cell identifier and a number of subbands allocated to the FP location for the uplink control channels, and transmitting a ranging signal based on the subband index for the ranging resource allocation. Thus, interference to a neighboring cell may be reduced in the ranging channel transmission.