Methods for performing change of primary cell during carrier aggregation operation are described. A mobile station (MS) receives a message to change a primary cell and to perform a random access communication with a new primary cell. Upon receiving a random access response message from the new primary cell, the MS starts transmitting a control channel to the new primary cell. In one embodiment, the MS releases the configuration of an uplink control channel and transmits uplink control information through an uplink shared channel. Upon completion of the primary cell change procedure, the MS starts transmission of an uplink control channel to the new primary cell.