A method and apparatus are provided for setting a neighbor in a Radio Network Controller (RNC) of a mobile communication system. The method includes receiving, from a Node B, a message indicating that a radio link is released; storing source cell information, when restoration of the radio link fails; receiving, from a User Equipment (UE), an RRC cell update message; storing target cell information included in the RRC cell update message; determining whether a neighbor of a source cell and a target cell is set, based on the source cell information and the target cell information; and setting the neighbor by using the source cell information and the target cell information if the neighbor is not set.