The dichotic presentation of two sinusoids with a slight difference in frequency elicits subjective fluctuations called binaural beat (BB). BBs provide a classic example of binaural interaction, considered to result from neural interaction in the central auditory pathway that receives input from both ears. To explore the cortical representation of the fluctuation of BB, we recorded magnetic fields evoked by slow BB of 4.00 or 6.66 Hz in nine normal subjects. The fields showed small amplitudes; however, they were strong enough to be distinguished from the noise accompanying the recordings. Spectral analyses of the magnetic fields recorded on single channels revealed that the responses evoked by BBs contained a specific spectral component of BB frequency, and the magnetic fields were confirmed to represent an auditory steady-state response (ASSR) to BB. The analyses of spatial distribution of BB-synchronized responses and minimum-norm current estimates revealed multiple BB ASSR sources in the parietal and frontal cortices in addition to the temporal areas, including auditory cortices. The phase of synchronized waveforms showed great variability, suggesting that BB ASSR does not represent changing interaural phase differences (IPD) per se, but instead it reflects a higher-order cognitive process corresponding to subjective fluctuations of BB. Our findings confirm that the activity of the human cerebral cortex can be synchronized with slow BB by using information on the IPD.