A method and apparatus are disclosed. In an example from the perspective of a User Equipment (UE), the UE initiates a first Early Data Transmission (EDT) in RRC_INACTIVE state. Responsive to initiating the first EDT, the UE initiates a Random Access (RA) procedure in a cell configured with a normal uplink (NUL) carrier and a supplementary uplink (SUL) carrier. The UE selects the SUL carrier or the NUL carrier for performing the RA procedure based on at least one of whether there are one or more available Physical Random Access Channel (PRACH) resources for EDT on the SUL carrier or whether there are one or more available PRACH resources for EDT on the NUL carrier.