We calculate Galactic Chemical Evolution (GCE) of Mo and Ru by taking into account the contribution from $ u p$-process nucleosynthesis. We estimate yields of $p$-nuclei such as $^{92,94}mathrm{Mo}$ and $^{96,98}mathrm{Ru}$ through the $ u p$-process in various supernova (SN) progenitors based upon recent models. In particular, the $ u p$-process in energetic hypernovae produces a large amount of $p$-nuclei compared to the yield in ordinary core-collapse SNe. Because of this the abundances of $^{92,94}mathrm{Mo}$ and $^{96,98}mathrm{Ru}$ in the Galaxy are significantly enhanced at [Fe/H]=0 by the $ u p$-process. We find that the $ u p$-process in hypernovae is the main contributor to the elemental abundance of $^{92}$Mo at low metallicity [Fe/H$]<-2$. Our theoretical prediction of the elemental abundances in metal-poor stars becomes more consistent with observational data when the $ u p$-process in hypernovae is taken into account.