A signal encoding apparatus and method of a radio frequency identification (RFID) reader capable of removing a high frequency component without using a digital filter, and performing Manchester encoding by using two symbols. The signal encoding apparatus of the RFID reader including an encoding unit that stores a first symbol and a second symbol; transmits the first symbol if data received after an initial state is zero (0), and returns to the initial state; delays for a given time period if the data received after the initial state is one (1); transmits the second symbol if data received after the delayed given time period is zero (0), and returns to the initial state; and transmits the first symbol if the data received after the delayed given time period is one (1), and stands by.