An apparatus and method for allocating a resource to a Mobile Station (MS) connected to a Relay Station (RS) in a broadband wireless communication system are provided. In the broadband wires communication system, a Base Station (BS) includes a transmitter for transmitting a pilot signal transmission request message to an MS, and a scheduler for frequency-selectively allocating a resource to the MS by using channel information upon receiving from an RS the channel information estimated using the pilot signal.