Disclosed is a reception apparatus and method of a mobile station in a Software Defined Radio (SDR) mobile communication system. A radio frequency (RF) processor converts a received RF signal into a digital signal, and outputs data on a per-unit basis according to a predetermined clock. An external memory stores the output data in a predetermined buffer area. A digital signal processing unit reads stored data samples and performs digital signal processing on the read data samples while storing the data in the external memory is completed.