Background: Non-alcoholic fatty liver disease (NAFLD) is currently the most common cause of chronic liver disease. Diet and lifestyle changes have dramatically increased its prevalence worldwide. This meta-analysis was performed to investigate the efficacy of physical activity intervention on liver-specific endpoints in the NAFLD population, namely hepatic enzyme levels, serum lipid levels, and glucose metabolism. Methods: PubMed and China National Knowledge Infrastructure (CNKI) databases were searched for randomized clinical trials of physical activity intervention on patients with NAFLD through to April 20, 2019. Effect sizes were reported as the standardized mean differences (SMD) and 95% confidence intervals (CI). The quality of the included studies was assessed using the Cochrane risk of bias tool. Meta-analyses were conducted using random-effect or fixed-effect models depending on the significance of heterogeneity. Clinical variability was investigated using subgroup analyses according to physical activity type and duration. Results: Eleven studies with a cumulative total of 1000 participants met the selection criteria. Physical activity was associated with small reductions in three hepatic enzyme parameters: alanine aminotransferase, (SMD: -0.17, 95% CI: -0.29 to -0.05), aspartate aminotransferase, (SMD: -0.25, 95% CI: -0.37, -0.13), and γ-glutamyl transferase (SMD: -0.21, 95% CI: -0.35, -0.08). Significant small improvements were also found for total cholesterol (SMD: -0.22, 95% CI: -0.34, -0.09), triglycerides (SMD: -0.20, 95% CI: -0.32 to -0.07), and low-density lipoprotein cholesterol (SMD: -0.26, 95% CI: -0.39 to -0.13). Physical activity also slightly improved two glucose metabolism parameters: fasting glucose (SMD: -0.25, 95% CI: -0.37 to -0.12) and homeostasis model assessment of insulin resistance (SMD: -0.38, 95% CI: -0.52, -0.24). High-density lipoprotein cholesterol and fasting insulin between the physical intervention group and control group were not significantly different. Subgroup analysis suggested that both aerobic exercise alone and resistance exercise alone could improve most liver function and glucose metabolism outcomes and that longer exercise duration generally had better improvement effects. The difference between all subgroups was not significant, except for the TG subgroups categorized by physical activity type. Conclusions: Our findings suggest that physical activity alone can only slightly improve hepatic enzyme levels, serum lipid levels, and glucose metabolism in patients with NAFLD.