Whey protein (WP) is a dairy food supplement and, due to its effects on fat-free mass (FFM) gain and fat mass (FM) loss, it has been widely consumed by resistance training practitioners. This review analyzed the impact of WP supplementation in its concentrated (WPC), hydrolyzed (WPH) and isolated (WPI) forms, comparing it exclusively to isocaloric placebos. Random effect meta-analyses were performed from the final and initial body composition values of 246 healthy athletes undergoing 64.5 ± 15.3 days of training in eight randomized clinical trials (RCT) collected systematically from five scientific databases. The weighted mean difference (WMD) was statistically significant for FM loss (WMD = −0.96, 95% CI = −1.37, −0.55, p < 0.001) and, in the analysis of subgroups, this effect was maintained for the WPC (WMD = −0.63, 95% CI = −1.19, −0.06, p = 0.030), with protein content between 51% and 80% (WMD = −1.53; 95% CI = −2.13, −0.93, p < 0.001), and only for regular physical activity practitioners (WMD = −0.95; 95% CI = −1.70, −0.19, p = 0.014). There was no significant effect on FFM in any of the scenarios investigated (p > 0.05). Due to several and important limitations, more detailed analyses are required regarding FFM gain.