Objective: The aim of this study was to make an indirect comparison of the results from meta-analyses that evaluated the severity of hot flushes in postmenopausal women exposed to hormone therapy (HT) or soy extracts. Methods: A systematic review and meta-analysis of HT and soy extracts related to the reduction of hot flushes in postmenopausal women versus the same control (placebo) were conducted. In addition, the combination of the overall results obtained from these two meta-analyses (indirect comparison) was adjusted to the common control (placebo). Results: The indirect standardized mean difference (SMD) obtained from the combination of both individual meta-analyses was calculated by using the following equation: SMD(indirect SOY vs HT) = SMD(soy) - SMD(HT), with a total indirect variance (var) equivalent to the following equation: var(total) = var(soy) + var(HT). These calculations yielded a point estimate of -0.84 (95% CI, -1.33 to -0.35) for the indirect SMD favorable to HT. Conclusions: HT and soy interventions showed a significant difference in efficacy for the reduction of hot flushes in postmenopausal women when each treatment was compared with placebo. However, using indirect comparison, there is a statistically significant difference between HT and soy extracts in their effects on hot flushes.