An apparatus for eliminating motion artifacts in a bio signal includes a bio signal acquisition unit configured to acquire a bio signal from a patient; a reconstruction signal generator configured to generate a reconstruction signal of the acquired bio signal based on a result of comparing the acquired bio signal with a bio signal pattern of the patient generated using a bio signal measured from the patient before acquiring the bio signal from the patient; and a motion artifact elimination unit configured to eliminate motion artifacts in the acquired bio signal based on a difference between the reconstruction signal and the acquired bio signal.