A method and apparatus is provided that controls the handover between distributed units (DUs) (inter-DU handover) in an eNB including a central unit (CU) and a DU. The method and system fuses 5G communication systems with IoT technology to transmission data at a high rate after 4G systems. The communication method and system is applied to intelligent services, based on 5G communication technology and IoT related technology, for example, smart homes, smart buildings, smart cities, smart cars or connected cars, health care, digital education, retail business, security, safety-related services, etc. The method includes transmitting, to a source DU of the base station, a first message instructing a handover; receiving, from the source DU, a second message including feedback information related to a packet data unit (PDU) transmitted from the source DU to a terminal; receiving, from a target DU of the base station, a third message including information on a random access of the terminal; and transmitting, to the target DU, downlink data, based on the second message, in response to the third message.