A method and an apparatus for controlling transmitter power of a femto base station in a broadband wireless communication system are provided. In the method, a femto base station receives a signal having an intensity of a threshold or more from UE and transmits a message reporting power-on of a transmitter to a femto base station controller. The UE transmits a message reporting downlink signal measurement results of femto base stations to the femto base station controller via a macro base station. The femto base station controller determines a femto base station which becomes a handover target of the UE using report messages of the femto base stations and the UE. The femto base station controller transmits a handover procedure start message to the macro base station and the determined femto base station.