A method in a base station for controlling a Random Access, RA, procedure is provided. The base station initiates (201) an RA procedure on a Secondary Cell, SCell, in a User Equipment, UE, by sending to the UE a Physical Downlink Control Channel, PDCCH, order for a RA procedure on the SCell. At initiation of RA, the base station starts (202) a timer in the base station. The timer is a timer for random access failure detection associated with said initiated RA procedure. If the RA procedure has not been completed before expiry of said timer, the base station sends (205) a command to the UE, commanding the UE to deactivate the SCell, and thereby stopping the RA procedure on the SCell.