A method and an apparatus for setting a quiet window in a passive optical network system are provided. A first response time from a time after an optical line terminal (OLT) transmits a serial number request up to a time in which the OLT receives a first response signal to the serial number request is measured, and a second response time up to a time in which the OLT receives a final response signal to the serial number request is measured. In addition, distance information of an optical network unit (ONU) including the first response time and the second response time is acquired.