Aim Bile acids are suggested to be involved in the antidiarrhetic effect of Goreisan (GRS). This study aimed to investigate the effect of GRS on fecal bile acid levels and composition of the gut microbiota in mice. Correlation analysis was employed to identify the potential gut microbiota associated with the alterations in fecal bile acid levels induced by GRS. Methods Male C57BL/6 mice were fed a diet supplemented with GRS water extract for 4 weeks. Feces and cecal contents were collected from the mice to determine bile acid levels and analyze bacterial composition. Results GRS administration significantly increased the levels of fecal secondary bile acids, including ω‐muricholic acid (MCA), hyodeoxycholic acid (HDCA), and lithocholic acid (LCA). In contrast, the levels of primary bile acids, such as β‐MCA, cholic acid (CA), and chenodeoxycholic acid (CDCA) showed a marked decrease. Further analysis revealed a positive correlation between the relative abundance of Alloprevotella, Dehalobacterium PAC001221, and Eubacterium g23 and fecal levels of ωMCA, HDCA, and LCA. Conclusions GRS was suggested to promote the formation of fecal secondary bile acids in mice, possibly through the enhancement of bacterial 7β‐dehydroxylation and 6β‐epimerization activities. These changes may be involved in the antidiarrhetic action of GRS. Concurrent evaluation of fecal bile acids and gut microbiota presents a promising approach for elucidating the novel mechanisms underlying the effects of kampo formulations, particularly in modulating the microbial metabolism of intestinal bile acids.