Objective: The aim of this study was to assess gut microbiota modifications after exercise in humans and animal models with obesity or type 2 diabetes and their role in exercise-induced weight loss. Methods: A systematic search of six databases was conducted on July 31, 2021. The extracted data on body fat or body weight from human and animal studies were analyzed using random-effects meta-analysis. Results: A total of 28 studies were included, with all studies reporting exercise-induced gut microbiota modifications; however, the modified taxa varied among studies. Proteobacteria was the only taxa reported to be altered by exercise in more than one human and one animal study. Taxa belonging to Firmicutes were the most responsive to exercise in humans and mice, whereas Proteobacteria taxa were the most responsive to exercise in rats. A meta-analysis was conducted to examine the weight-lowering effect of exercise based on data subgrouped by altered or unaltered α-diversity or β-diversity. The association between the weight-lowering effect of exercise and altered β-diversity was observed in humans with obesity but not in animals. Conclusions: These findings suggest that gut microbiota modifications contribute to exercise-induced weight loss in obesity; however, their precise contributions, especially those of taxon-level variations, remain to be investigated.