Pd-Cu alloys are of particular interest for use as hydrogen purification membranes, and identifying the effects of stoichiometry on hydrogen permeability is the key to exploring the possibility of improving this material. In this study, we carried out hydrogen permeation tests for Pd-51.5 mol%Cu alloy in order to understand the effects of excess Cu atoms on the hydrogen permeability of Pd-Cu alloys with B2-type crystal structure. Even though the Pd-51.5 mol%Cu alloy contained a small amount of a face-centered cubic phase, its hydrogen permeability was higher than that of practical Pd-53 mol%Cu alloy with a B2 single phase in the temperature range of 298 K to 623 K. These results were analyzed according to the consistent description of hydrogen permeation based on hydrogen chemical potential. It was found that the hydrogen solubility was improved by reducing the excess Cu atoms. On the other hand, the hydrogen diffusivity of Pd-51.5 mol%Cu alloy was still comparable to that of Pd-53 mol%Cu alloy and decreased significantly at low temperatures, just like that of the practical alloy. First-principles calculations suggested that the excess Cu atoms act as repellers and reduce the hydrogen solubility in the alloy, in a manner consistent with experimental results. It was also suggested that the excess Cu atoms reduce the apparent hydrogen diffusivity as the hydrogen atoms rarely occupy the interstitial sites around the excess Cu atoms. However, no significant differences in the hydrogen diffusivity due to the excess Cu atoms were observed in the experiment. Therefore, other factors apart from the excess Cu atoms may have inhibited the hydrogen diffusivity at low temperatures. Our findings will serve as a basis for enhancing the hydrogen permeability of Pd-Cu alloys by tuning their composition and processing.