An apparatus and method for generating and parsing a MAC PDU in a mobile communication system are provided in which LCIDs of MAC SDUs to be multiplexed are checked, the length of an LF is determined for each of the MAC SDUs, referring to LF lengths predetermined for the LCIDs, a MAC header including the LCIDs and LFs of the determined lengths for the MAC SDUs is generated, and a MAC PDU is generated by attaching the MAC header to payload including the MAC SDUs. During the MAC header generation, if a padding size required for the MAC PDU generation calculated taking into account the absence of a last LF in the MAC header is larger than the length of the last LF, the last LF is included in the MAC header, the required padding size is recalculated, taking into account the inclusion of the last LF, and a padding is added according to the re-calculated padding size.