S‐wave attenuation characteristics of sediments are important for accurate prediction of ground motion. High‐quality borehole seismic observation data have been accumulated in Japan since the construction of KiK‐net, a nationwide network, in the early 2000s. We estimated S‐wave attenuation () values in sediments by applying a new deconvolution method to KiK‐net data. First, incident and surface‐reflected waves from local earthquakes are separated by deconvolving the seismogram from the bottom of the borehole with the seismogram from the ground surface. Then, values of sediments are estimated from transfer functions (or system functions) between incident and surface‐reflected waves that are stacked with respect to available earthquakes. Applying the deconvolution method to the records from KiK‐net stations having boreholes deeper than 300 m, we obtained stable estimates of values in the 0.5–10 Hz range at 16 stations. The values decrease with frequency up to about 2–3 Hz but become nearly constant at higher frequencies. By fitting a power‐law function to the values at frequencies lower than 2 Hz, values at 1 Hz ranged from 0.02 to 0.2, and the exponent of the power law ranged from −0.12 to −1.00. The obtained values show clear depth dependence. Our results are consistent with values estimated by previous studies, which supports the usefulness of our new method.