An apparatus and a method for handover between a broadband wireless communication system and a heterogeneous communication system are provided. An operating method of a base station for the handover between a broadband wireless communication system and a and a heterogeneous communication system includes when a terminal enters a border cell, sending a message requesting to measure a signal level of a downlink, to the terminal, when a signal level measured by the terminal falls below a preset threshold, requesting a handover, to a corresponding heterogeneous communication system, over a core network, receiving a message, including channel allocation information for the handover, from the corresponding heterogeneous communication system, and forwarding the message, including the channel allocation information, to the terminal. Hence, when the terminal gets out of the service coverage area of the broadband wireless communication system, it can be handed over to the heterogeneous communication system seamlessly.