An apparatus and method for transmitting/receiving system information in a wireless communication system with a hierarchical cell structure are provided. A method for transmitting system information in a micro Base Station (BS) in a wireless communication system in which at least one micro cell exists within a macro cell includes transmitting first system information to a Mobile Station (MS) communicating with a macro BS within a micro cell and an MS communicating with a micro BS within the micro cell, and transmitting second system information to the MS communicating with the micro BS within the micro cell.