A method and apparatus are disclosed. In an example from the perspective of a User Equipment (UE), the UE maintains a first counter and a second counter, wherein the first counter and the second counter are associated with a Special Cell (SpCell) and are for counting beam failure instance indications. The UE initiates a first beam failure recovery (BFR) procedure based on the first counter being equal to or larger than a value, wherein the first BFR procedure includes initiating a random access procedure for SpCell BFR associated with the SpCell. The UE sets the first counter and the second counter to a defined value in response to completion of the first BFR procedure.