Non-alcoholic fatty liver disease (NAFLD) is a widespread threat to human health. However, the present screening methods for NAFLD are time-consuming or invasive. The present study aimed to assess the potential of microRNAs (miRNAs/miRs) in serum extracellular vesicles (EVs) as a biomarker of NAFLD. C57BL/6J mice were fed either a 12-week high-fat diet (HFD) or standard chow to establish NAFLD and control groups, respectively. Serum samples were obtained from the mouse model of NAFLD, as well as 50 patients with NAFLD and 50 healthy individuals, and EVs were extracted and verified. Using reverse transcription-quantitative PCR, the mRNA expression level of selected miRNAs in the serum and EVs was analyzed. In order to determine the diagnostic value, receiver operating characteristic (ROC) curves were used. The mice treated with HFD showed notable hepatic steatosis and higher concentrations of serum alanine aminotransferase (ALT). There was also a significant decrease in the expression levels of miR-135a-3p, miR-129b-5p and miR-504-3p, and an increase in miR-122-5p expression levels in circulating EVs in mice treated with HFD and patients with NAFLD. There were also similar miR-135a-3p and miR-122-5p expression patterns in the serum. ROC analysis demonstrated that miR-135a-3p in circulating EVs was highly accurate in diagnosing NAFLD, with the area under the curve value being 0.849 (95% CI, 0.777-0.921; P<0.0001). Bioinformatics analysis indicated that dysregulated miR-135a-3p was associated with 'platelet-derived growth factor receptor signaling pathway' and 'AMP-activated protein kinase signaling pathway'. In summary, circulating miR-135a-3p in EVs may serve as a potential non-invasive biomarker to diagnose NAFLD. This miRNA was a more sensitive and specific biological marker for NAFLD compared with ALT.