A method and apparatus are disclosed from the perspective of a UE (User Equipment). In one embodiment, the method includes the UE receiving an SCell activation/deactivation MAC (Medium Access Control) control element to activate the SCell. The method further includes the UE activates the SCell based on the SCell activation/deactivation MAC control element. The method also includes the UE receiving a beam indication by a MAC control element via the PCell, wherein the beam indication includes a cell index and the beam indication is used to derive at least one beam to be used in the SCell. In addition, the method includes the UE using the at least one beam for a DL (Downlink) transmission or an UL (Uplink) transmission in the SCell.