A method and an apparatus for activating and deactivating secondary cells in a carrier aggregation environment are provided. In one embodiment, a Medium Access Control (MAC) Control Element (CE) command is received from a base station for activating/deactivating a secondary cell associated with a User Equipment (UE). The secondary cell configured for the UE is activated/deactivated based on the MAC CE command. Further, a first uplink grant is received from the base station upon activation/deactivation of the secondary cell. Accordingly, quality information (e.g., channel quality information, sounding reference signal information, and the like) associated with the cell(s) is transmitted to the base station in the received first uplink grant over a physical uplink shared channel. Furthermore, a hybrid automatic repeat request entity associated with the secondary cell is reset.