We aim to systematically review the efficacy of prebiotics in reducing anthropometric and biochemical parameters in individuals with non-alcoholic fatty liver disease (NAFLD). A systematic search using PubMed/MEDLINE, Embase, clinicaltrials.gov, Cinahl, and Web of Science of articles published up to 20 March 2020 was performed for randomized controlled trials enrolling >20 adult patients. Random-effect meta-analysis for metabolic outcomes in NAFLD patients was performed for anthropometric data in addition to liver enzyme, carbohydrate, and lipid parameters. We found six trials (comprising a total of 242 patients) with NAFLD, with subjects aged 38–52 years. The mean time of fiber administration varied between 10 and 12 weeks. The main fiber types were psyllium (seeds or powder), Ocimum basilicum (seeds), and high-performance inulin and oligofructose powder at doses of either 10 or 16 g per day. The control group received either maltodextrin (powder or capsules) or crushed wheat (powder). Patients on the diet with added fiber had improvements in body mass index (BMI) (standardized mean difference (SMD) = −0.494, 95% confidence interval (CI): −0.864 to −0.125, p = 0.009); alanine aminotransferase (ALT) (SMD = −0.667, 95% CI: −1.046 to −0.288, p = 0.001); aspartate aminotransferase (AST) (SMD = −0.466, 95% CI: −0.840 to −0.091, p = 0.015); fasting insulin (SMD = −0.705, 95% CI: −1.115 to −0.295, p = 0.001); and homeostasis model assessment for insulin resistance (HOMA-IR) (SMD = −0.619, 95% CI: −1.026 to −0.211, p = 0.003). Hence, the results show that fiber supplements result in favorable changes as reflected in the measurement of anthropometric, metabolic, and liver-related biomarkers, i.e., body mass index (BMI), homeostasis model assessment for insulin resistance (HOMA-IR), insulin, alanine aminotransferase (ALT), and aspartate aminotransferase (AST). These effects suggest the potential benefits of fiber consumption for NAFLD populations. More prospective, controlled studies should be conducted to reveal specific details regarding the fiber type, dosage, and duration for optimal intervention.