A method for handling an uplink grant received on a physical downlink control channel (PDCCH) in a user equipment (UE) of a wireless communication system is disclosed. The method includes steps of setting a Temporary Cell Radio Network Temporary Identifier (Temporary C-RNTI) of the UE to a value assigned in a Random Access Response message, monitoring a contention resolution message, receiving an uplink grant on PDCCH addressed to the Temporary C-RNTI, and not using the uplink grant to transmit data if the uplink grant corresponds to a Hybrid Automatic Repeat Request (HARQ) Process different from an HARQ Process used for transmission of a MediumAccess Control (MAC) Protocol Data Unit (PDU) in a Message 3 buffer.