Hydrogen (H) is a common impurity in metals and has a significant effect on their purification, even at concentrations of only a few parts per million. Here we present a comparative analysis of the behaviors of H in Au and Ag based on first-principles calculations. In bulk Au and Ag, the results demonstrate that the tetrahedral position is energetically more stable for a single H atom than the octahedral site. The concentration of H dissolving in the interstitial sites as a function of temperature is calculated in both metals. To characterize the dynamic behaviors, in bulk Au and Ag we determine the theoretical diffusivity and permeation of H, which are in quantitative agreement with the experimental data. Further, we investigate the role of vacancy on the formation of the Hn–vacancy (HnV) via a clustering reaction. One vacancy can accommodate up to 9 H atoms in Au and capture as many as 7 H atoms in Ag. The H2 molecule in the vacancy is energetically unstable in both metals. These research results will provide a very useful reference for the refinement of Ag/Au as noble metals in industry.