We synthesize two Nb/C composites with an order of magnitude difference in the density of single niobium atoms substituted into defective graphitic layers. The concentration and sites of single Nb atoms are identified using aberration-corrected scanning transmission electron microscopy and density functional theory. Comparing the experimental complex permittivity spectra reveals that a representative dielectric resonance at ∼16 GHz originates from the intrinsic polarization of single Nb atom sites, which is confirmed by theoretical simulations. The single-atom dielectric resonance represents the physical limit of the electromagnetic response of condensed matter, and thus might open up a new avenue for designing electromagnetic wave absorption materials. Single-atom resonance also has important implications in understanding the correlation between the macroscopic dielectric behaviors and the atomic-scale structural origin.