A method of controlling a Forward Error Correction (FEC) operation including: configuring a FEC frame to be transmitted between an OLT and an ONU comprising a FEC frame identifier indicating whether FEC should be performed, data, a first flag indicating that FEC should be performed, and a second flag indicating that the FEC frame is to be FEC encoded; initializing the OLT by disabling a FEC function; determining whether the ONU requires FEC to be performed based on a FEC frame identifier received from the ONU; IPG stretching the FEC frame when the ONU requires to FEC to be performed; and transmitting the FEC frame to the ONU after FEC encoding based on the second flag of an input frame to a PCS sublayer from an upper layer. The method controls an effective operation of a FEC of an ONU and an OLT without changing a Round Trip Time (RTT) according to optical link quality in an EPON. Accordingly, FEC is used only if necessary, thereby simplifying the managing of a link, and preventing an excessive 35% reduction of throughput caused by use of unnecessary FEC.