An apparatus and method for allocating resources in an Single Carrier-Frequency Division Multiple Access (SC-FDMA) communication system are provided, in which a Node B determines on a cell basis whether to turn or off inter-subband hopping and whether to turn on or off mirroring for a resource unit for the UE on a frequency axis along which at least two subbands are defined, at set hopping times, selects a resource unit by selectively performing inter-subband hopping and mirroring on the resource unit for the UE according to the determination, and allocates the selected resource unit to the UE.