A method and apparatus of measuring a packet throughput using a timer in a wireless communication system are provided. When determining a reference time for estimating packet throughput, a receiver determines the time that a data burst starts or ends using a timer in order to estimate the packet throughput considering a change in the data burst of the transmitter buffer. A measurement period is defined through the determined start time and end time of the data burst by the timer, and packet throughput is measured considering the total amount of the received data burst. The throughput of packet data may be estimated by each base station based on the same standard rule, so that the measured packet throughput values may be reliable, thus allowing the operator to make use of it as a parameter for MDT.