While functional connectivity in the human cortex has been increasingly studied, its relationship to cortical representation of sensory features has not been documented as much. We used functional magnetic resonance imaging to demonstrate that voxel-by-voxel intrinsic functional connectivity (FC) is selective to frequency preference of voxels in the human auditory cortex. Thus, FC was significantly higher for voxels with similar frequency tuning than for voxels with dissimilar tuning functions. Frequency-selective FC, measured via the correlation of residual hemodynamic activity, was not explained by generic FC that is dependent on spatial distance over the cortex. This pattern remained even when FC was computed using residual activity taken from resting epochs. Further analysis showed that voxels in the core fields in the right hemisphere have a higher frequency selectivity in within-area FC than their counterpart in the left hemisphere, or than in the noncore-fields in the same hemisphere. Frequency-selective FC is consistent with previous findings of topographically organized FC in the human visual and motor cortices. The high degree of frequency selectivity in the right core area is in line with findings and theoretical proposals regarding the asymmetry of human auditory cortex for spectral processing.