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 performs inter-subband hopping on a resource unit for a User Equipment (UE) on a frequency axis along which at least two subbands are defined, at each predetermined hopping time, determines whether to turn on or off mirroring in a subband having the hopped resource unit on a cell basis at the each hopping time, selects a resource unit by selectively mirroring the hopped unit according to the determination, and allocates the selected resource unit to the UE.