An apparatus and method for setting a guard band with respect to an asynchronous Base Station (BS) in a broadband wireless communication system are provided. The BS includes a controller for generating a control signal to set a guard band when a time offset occurs between BSs; a mapper for mapping and outputting transmit data to a band, excluding the guard band, of a unique band of the BS according to the control signal; and an operator for multicarrier-modulating data fed from the mapper.