Background: Nonalcoholic fatty liver disease (NAFLD) has become prevalent in recent decades, especially in developed countries, and approaches for the prevention and treatment of NAFLD are not clear. The aim of this research was to analyze and summarize randomized controlled trials that investigated the effects of probiotics on NAFLD. Methods: Seven databases (PubMed, Embase, the Web of Science, the Cochrane Library, China National Knowledge Infrastructure, Wan Fang Data, and VIP Database) were searched. Then, eligible studies were identified. Finally, proper data extraction, synthesis and analysis were performed by trained researchers. Results: Anthropometric parameters: with use of probiotics weight was reduced by 2.31 kg, and body mass index (BMI) was reduced by 1.08 kg/m2. Liver function: probiotic treatment reduced the alanine aminotransferase level by 7.22 U/l, the aspartate aminotransferase level by 7.22 U/l, the alkaline phosphatase level by 25.87 U/l, and the glutamyl transpeptidase level by −5.76 U/l. Lipid profiles: total cholesterol, low-density lipoprotein cholesterol, and triglycerides were significantly decreased after probiotic treatment. Their overall effects (shown as standard mean difference) were −0.73, −0.54, and −0.36, respectively. Plasma glucose: probiotics reduced the plasma glucose level by 4.45 mg/dl and the insulin level by 0.63. Cytokines: probiotic treatment decreased tumor necrosis factor alpha by 0.62 and leptin by 1.14. Degree of liver fat infiltration (DFI): the related risk of probiotics for restoring DFI was 2.47 (95% confidence interval, 1.61–3.81, p < 0.001). Conclusion: Probiotic treatment or supplementation is a promising therapeutic method for NAFLD.