A method of operating an ESS with optimal efficiency includes: collecting charge/discharge efficiency data of a PCS; collecting charge/discharge efficiency data of a battery depending on current state of charge of the battery; creating charge/discharge efficiency data of a unit BESS including the PCS and the battery by using the collected data; determining optimal charge/discharge levels of at least two unit-BESSs included in the ESS by using charge/discharge efficiency data of the at least two unit-BESSs to satisfy commanded input/output power values of the whole ESS at a current point of time; and charging or discharging the at least two unit-BESSs depending on the determined optimal charge/discharge power values.