A method and apparatus are disclosed from the perspective of a User Equipment (UE). In one embodiment, the method includes receiving a Random Access Channel (RACH) configuration from a network node, wherein the RACH configuration indicates at least one Physical Random Access Channel (PRACH) resource for beam failure recovery. The method further includes receiving a timing advance command from the network node, and starting or restarting a time alignment timer when receiving the timing advance command. The method also includes releasing the at least one PRACH resource for the beam failure recovery indicated by the RACH configuration when the timing alignment timer expires.