Provided are a method and apparatus for scheduling in a carrier aggregation system. The method includes: transmitting information for indicating a plurality of secondary cells to be scheduled through a joint coded control channel by using a higher layer signal; transmitting a separate coded control channel for scheduling a primary cell; and transmitting one joint coded control channel for scheduling the plurality of secondary cells, wherein the separate coded control channel is a control channel for scheduling one data channel transmitted through the primary cell, and the joint coded control channel is a control channel for scheduling the plurality of data channels transmitted through the plurality of secondary cells.