A method and apparatus are disclosed from the perspective of a User Equipment (UE), wherein the UE is configured with multiple Bandwidth Parts (BWPs). In one embodiment, the method includes the UE receiving information from a network node to associate a RACH (Random Access Channel) configuration with a BWP among the multiple BWPs. The method further includes that the UE performing a RACH transmission in the BWP using the RACH configuration associated with the BWP.