A method and apparatus for using a guard band as a data subcarrier in a communication system supporting frequency overlay are provided. In a method of operating mobile station for using a guard band as a subcarrier for signal transmission in a communication system supporting frequency overlay, the method includes searching for a first center frequency located at a position corresponding to an integer multiple of a subcarrier spacing, after searching for the first center frequency, receiving information indicating the numbers n1 and n2 of first additional subcarriers, and performing a first network entry process by using all subcarriers including the first additional subcarriers.