A cellular station with a wireless module and a controller module is provided for handling random access procedures in a multi-carrier system. The wireless module performs wireless transceiving to and from a mobile communication device on a first SCell and a second SCell of a timing reference group. The controller module waits for a predetermined period of time subsequent to an expiry of a deactivation timer for the first SCell maintained in the cellular station, and transmits, to the mobile communication device via the wireless module, a PDCCH order for initiating a random access procedure on the second SCell or an activation command for activating the first SCell, in response to the predetermined period of time being elapsed.