Defining the reference rock or soil condition related to ground‐motion prediction is an important aspect of seismic‐hazard analysis. In a previous study by the authors, a method was proposed to establish a reference rock profile for Switzerland through the comparison of empirical amplification functions with shear‐wave velocity profiles at 27 selected sites of the Swiss National Seismic Network. The retrieved velocity profile served as reference for a regional ground‐motion prediction equation. However, a lacking piece of information remained: the anelastic attenuation for such a reference profile. Reference attenuation is essential to correctly model and interpret amplification at high frequencies. In the present study we extended our approach to simultaneously model both the reference shear‐wave velocity profile and the corresponding attenuation for Japan. We compared site‐specific attenuation measurements with quarter‐wavelength average velocities at 36 soil and rock sites from the Japanese KiK‐net strong‐motion network. The selected sites are characterized by a lack of observed resonance phenomena in order to avoid trade‐off between amplification and attenuation effects. We establish a parametric model through regression analysis. The resulting model gives us the possibility to estimate anelastic attenuation of a rock site with a given velocity profile and provides the base for host‐to‐target adjustments of real or modeled ground motion.