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Aim: Gingyogedokusan (GGGS) is a herbal medicine approved for upper respiratory infections in Japan, and could be utilized for the treatment of influenza. We conducted a multi‐center, prospective trial, comparing GGGS against oseltamivir in patients with influenza, but failed to include enough participants for conventional analysis. We further conducted a Bayesian analysis, however, using the Markov chain Monte Carlo (MCMC) method, by utilizing our original data. Methods: We used our data from 2010 and 2011, which compared GGGS and oseltamivir. A total of 10 patients were diagnosed with influenza and enrolled in the study (six for GGGS and four for oseltamivir). We conducted MCMC to elucidate posterior distributions for outcomes. Outcomes were time to alleviation of symptoms, time to recovery of activity level, time to recovery of health status, and time to resolution of fever. Results: Calculated mean time to alleviate symptoms was 3.99 days for GGGS, while it was 5.66 days in the oseltamivir group (difference of 1.66 days, 95% credible interval: −3.64 to 6.46). The posterior probability of the mean time for the oseltamivir group being longer than that for the GGGS group was 69%. Likewise, that probability was 81% for recovery of activity level, 86% for health status, and 24%, for fever resolution. Conclusion: According to Bayesian analysis, GGGS appears to have superiority over oseltamivir in resolving symptoms, although fever may resolve earlier with oseltamivir use. This is a proof of concept study, to encourage further research into the efficacy of GGGS for the treatment of influenza. [ABSTRACT FROM AUTHOR]