An apparatus and method for estimating and combining frequency errors in a mobile communication system. A controller divides data received from a main base station (BS) and control information received from a neighbor BS and controls allocation to fingers. A main automatic frequency control (AFC) loop is formed by estimating and combining frequency errors of the data received from the main BS. A sub AFC loop is formed by subtracting a corrected value of the main AFC loop after estimating and combining frequency errors of the control information received from the neighbor BS.