This study examined the dynamic behavior of butanethiolate (SC4H9)-protected gold–silver 38-atom alloy clusters ([Au38–xAgx(SC4H9)24]0) in solution using reversed-phase high-performance liquid chromatography and electrospray ionization mass spectrometry. The results revealed that [Au38–xAgx(SC4H9)24]0 synthesized by reacting [Au38(SC4H9)24]0 with an Ag(I)–SC4H9 complex, which is the most frequently used method to synthesize gold–silver alloy clusters, continue to undergo intercluster metal exchange even after the distribution of the chemical composition of the clusters looks unchanged in the mass spectrum. The frequency of this intercluster metal exchange in solution varied depending on the standing time in solution and the synthesis method of [Au38–xAgx(SC4H9)24]0. These findings should be taken into consideration in future studies to realize deeper understanding of the physical and chemical properties of thiolate-protected gold–silver alloy clusters in solution.