We present a ground‐motion prediction equation for the vertical ground motions from subduction slab earthquakes in Japan using site class as the site term. Site classes are still useful because they are still used in some design codes and can be inferred from horizontal‐to‐vertical spectral ratios (Zhao, Irikura, et al., 2006). We find that removing records from sites with inferred site class improved the model goodness of fit. In the final model, all records are from sites with a measured shear‐wave velocity profile down to the engineering bedrock. The linear magnitude‐scaling rate for events with moment magnitude in the model for the vertical component (referred to as VC model) is larger than that for the horizontal component (referred to as HC model) at short spectral periods up to 0.2 s and similar at the other periods. The magnitude‐scaling rate for events with an for the VC model is smaller than that for the HC model at short periods up to 0.3 s and is considerably smaller than that for the HC model for other periods. The magnitude‐squared terms from the HC and VC models are comparable at all periods. The effect of volcanic path is significant at most spectral periods and the absolute values are less than those for the HC model. We find that the VC model standard deviations are larger than those of the HC model at short periods up to 0.08 s and are less than those of the HC model in the 0.1–1.25 s period range, whereas they are similar at spectral periods above 1.25 s. The generalized single‐station standard deviation for the VC model is larger than that of the HC model at short periods up to 0.07 s and they are very similar at the other periods.