SUMMARY The within-site variability in site response is the randomness in site response at a given site from different earthquakes and is treated as aleatory variability in current seismic hazard/risk analyses. In this study, we investigate the single-station variability in linear site response at K-NET and KiK-net stations in Japan using a large number of earthquake recordings. We found that the standard deviation of the horizontal-to-vertical Fourier spectral ratio at individual sites, that is single-station horizontal-to-vertical spectral ratio (HVSR) sigma σHV,s, approximates the within-site variability in site response quantified using surface-to-borehole spectral ratios (for oscillator frequencies higher than the site fundamental frequency) or empirical ground-motion models. Based on this finding, we then utilize the single-station HVSR sigma as a convenient tool to study the site-response variability at 697 KiK-net and 1169 K-NET sites. Our results show that at certain frequencies, stiff, rough and shallow sites, as well as small and local events tend to have a higher σHV,s. However, when being averaged over different sites, the single-station HVSR sigma, that is σHV, increases gradually with decreasing frequency. In the frequency range of 0.25–25 Hz, σHV is centred at 0.23–0.43 in ln scales (a linear scale factor of 1.26–1.54) with one standard deviation of less than 0.1. σHV is quite stable across different tectonic regions, and we present a constant, as well as earthquake magnitude- and distance-dependent σHV models.