A method of controlling congestion in a base station of a wireless communication system is provided. The method includes receiving a Service Data Unit (SDU) that includes pieces of data forwarded through a caching proxy, driving a timer each time an SDU is received for processing the SDU using a communication protocol, determining whether the SDU has been processed using the communication protocol until expiration of the timer, and controlling a transmission rate of the caching proxy based on a number of SDUs consecutively discarded or a number of SDUs consecutively transmitted depending on whether the timer has expired.