An apparatus and method for reordering data packets in a communication system are provided. The method includes detecting that a first time value of a timer used for reordering data packets needs to be set when a missing data packet occurs in receiving data packets, and, when the timer restarts, setting the first time value to a time value determined by compensating for a second time value which is used when the timer starts. The timer starts when a first Transmission Sequence Number (TSN) of a received data packet is greater than a TSN of a data packet which is expected to be received immediately after data packets received already and when the timer is not in an active state. The timer expires at a point of time when the second time value lapses. The timer stops when a data packet with the same TSN as the first TSN is sent as a reassembly entity before the expiring of the timer. The timer restarts when a received data packet which cannot be sent as the reassembly entity is buffered in a buffer after the stopping or the expiring of the timer.