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Purpose Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease which has become a public health concern, whose growing prevalence has been reported as around 33.9% in Iran. As oxidative stress plays a crucial role in the pathogenesis of NAFLD, antioxidant compounds such as quercetin could ameliorate the side effect of oxidative stress. The aim of the current study was to assess the effect of quercetin on lipid profile, liver enzymes and inflammatory indices in NAFLD patients. Design/methodology/approach In a randomized, double-blind, placebo-controlled trial conducted as a pilot study, 90 patients with NAFLD were supplemented with either a quercetin or a placebo capsule twice daily (500 mg) for 12 weeks. Both groups were advised to follow an energy-balanced diet with physical activity recommendations. Blood sample was obtained for laboratory parameters at baseline and the end of week 12. Findings At the end of the follow-up, quercetin group had significantly greater reduction in anthropometric parameters, cholesterol (−15 ± (−41, 0.00) in Q group versus −1± (−8, 2) in control group, p = 0.004), TG (−56.7 ± 22.7) in Q group versus −13.4 ± 27.7 in control group, p = 0.04), and tumor necrosis factor-α (TNF-α) (−49.5 ± (−99, 21) in Q group versus −5 ± (−21, 0.30) in the control group, p < 0.0001) compared to the control group. However, changes in fatty liver grade, liver enzymes, as well as high density lipoprotein-cholesterol and high-sensitivity C-reactive protein were not significantly different between the two groups. Originality/value To the best of the authors’ knowledge, this was the first study which assessed the effect of quercetin supplementation on liver enzymes, lipid profile and inflammatory indices of NAFLD patients as a double-blind placebo-controlled pilot study.