A method and an apparatus for transmitting a control channel when cells have different duplex structures in an intra-cell carrier aggregation system are provided. The method of transmitting and/or receiving a control channel by an evolved Node B (eNB) in a wireless communication system includes receiving capability information of a User Equipment (UE) from the UE, transmitting scheduling information to the UE, transmitting downlink data according to the transmitted scheduling information, and receiving an uplink control channel for the downlink data from the UE based on the capability information of the UE.