A method for beam failure recovery (BFR) by a user equipment (UE) is disclosed. The method includes receiving, by the UE, an instruction for BFR from a base station, and selecting, by the UE, at least one of a plurality of secondary cells (SCells) to perform BFR based on the instruction. The instruction is contained in a radio resource control (RRC) message, a medium access control (MAC) control element (CE) (MAC-CE), or downlink control information (DCI).