An apparatus and method determines neighbor Base Station (BS) information in a wireless communication system where a macro cell and a Femto cell coexist. The method includes, when a preamble scanning duration arrives, acquiring preamble information on at least one neighbor BS through preamble scanning. It is determined whether to scan a header for at least one neighbor BS among neighbor BSs for which the preamble information are acquired, in consideration of at least one of the acquisition or non-acquisition of new preamble information through the preamble scanning and a variation of an environment of a preamble acquired through the preamble scanning. And, in case that it is determined to scan the header, a header for a corresponding neighbor BS is scanned and header information of the neighbor BS is acquired.