A highly precise clock synchronization apparatus in a real-time locating system (RTLS), includes an optical transmitting/receiving unit for receiving a clock information frame from a clock synchronization server, converting the received clock information frame in series-parallel, and transmitting/receiving the clock information data and the clock information; an offset estimation unit for detecting a preamble signal and a clock information signal from the series-parallel converted clock information frame, calculating a phase difference value by comparing the detected preamble signal with the detected clock information signal, and outputting an offset value based on the calculated phase difference value; and a clock synchronization unit for updating a local clock value to a time of the clock synchronization server based on the offset value and the clock information frame.