Acute diarrhea is a burdensome disease with potentially harmful consequences, especially in childhood. Despite its large use in clinical practice, the efficacy of the probiotic Bacillus clausii in treating acute childhood diarrhea remains unclear. Our objective was to systematically review the efficacy of Bacillus clausii in the treatment of acute childhood diarrhea. The following electronic databases were systematically searched up to October 2017: MEDLINE (via PubMed/OVID), EMBASE (via OVID), Cochrane Central Database of Controlled Trials (via CENTRAL), Google Scholar, and ClinicalTrials.gov. Only randomized controlled trials were included. The overall effect for the meta-analysis was derived by using a random effects model. Six randomized controlled trials (1298 patients) met the eligibility criteria. Data arising from pooled analysis showed that Bacillus clausii significantly reduced the duration of diarrhea (mean difference = -9.12 h; 95% confidence interval [CI]: -16.49 to -1.75, p = 0.015), and the duration of hospitalization (mean difference = -0.85 days; 95% CI: -1.56 to -0.15, p = 0.017), compared with control. There was a trend of decreasing stool frequency after Bacillus clausii administration compared with the control group (mean difference = -0.19 diarrheal motions; 95% CI: -0.43 to -0.06, p = 0.14). Bacillus clausii may represent an effective therapeutic option in acute childhood diarrhea, with a good safety profile.