In this work, we have performed the first-principles calculations to investigate the Schottky barrier height (SBH) of various nanostructured silicide-silicon junctions. As for the silicides, PtSi, NiSi, TiSi2, and YSi2 have been used. We find that EFiF = EFi – EF, where EFi and EF are the intrinsic Fermi level of the semiconductor part and the Fermi level of the junction, respectively, is unchanged by nanostructuring. From this finding, we suggest a model, a symmetric increase of the SBH (SI) model, to properly predict SBHs of nanostructured silicide-silicon junctions. We also suggest two measurable quantities for the experimental validation of our model. The effect of our SI model applied to nanostructures such as nanowires and ultra-thin-bodies is compared with that of the widely used previous SBH model.