A method and apparatus for transmitting control information in a wireless communication system supporting carrier aggregation (CA) is disclosed. A method for transmitting control information to a base station (BS) by a user equipment (UE) in a wireless communication system includes receiving at least one of a physical downlink control channel (PDCCH) and a physical downlink shared channel (PDSCH) from the base station through at least one serving cell configured in the user equipment, and transmitting control information regarding PDCCH reception or PDSCH reception indicated by the PDCCH to the base station. The control information is transmitted through a physical uplink control channel (PUCCH) of a primary cell, using control information feedback timing of at least one of the primary cell and a first cell of the at least one serving cell, and the at least one serving cell uses different uplink and downlink (UL-DL) configurations.