An apparatus and method for operating a centralized Base Station (BS) in a mobile communication system are provided. An operation method of a remote radio unit in a separate type BS of a mobile communication system includes receiving channel state information transmitted by a terminal and transmitting the channel state information to a digital unit, performing scheduling using the channel state information, deciding data to be transmitted based on its own scheduling result and a scheduling result received from the digital unit, and providing the data to be transmitted to a modulator/demodulator (modem).