An apparatus and method for delay time computation and delay compensation between a Base Station (BS) and a remote Radio Frequency (RF) unit in a broadband wireless access system are provided. In a method of operating an apparatus for determining a delay time to compensate for delay between a BS modem card and a remote RF unit in a wireless access system, the method includes determining a process delay time required when traffic data is output from the BS modem card to an antenna of the remote RF unit in a state where a reference cable having a length short enough to neglect a cable delay time is connected between the BS modem card and the remote RF unit, determining a cable delay time required when a sync pulse signal is transmitted through a cable used in actual system operation between the BS modem card and the remote RF unit, and determining a time for outputting traffic data at an earlier time from a modem included in the BS modem card by using the determined process delay time and cable delay time.