In this study, we aim to investigate whether shikonin prevents against NAFLD. After feeding high-fat diet (HFD) for 10 weeks, Sprague-Dawley rats were received different doses of shikonin (5mg/kg/day, 10mg/kg/day and 20mg/kg/day) by gavage for the last 12 weeks of a total of 22 weeks of a HFD. Our results showed that total cholesterol (TC), triacylglycerol (TG), low-density lipoprotein cholesterol, aspartate aminotransferase and alanine aminotransferase were significantly increased, while high-density lipoprotein cholesterol was decrease, accompanied by hepatic injury and lipid accumulation in HFD-fed rats. Shikonin treatment attenuated the above biochemical and histopathological changes. Similarly, HFD-induced the increase of hepatic TC and TG levels were also ameliorated by shikonin treatment. Furthermore, shikonin observably mitigated HFD-induced the liver fibrosis and the increase of plasminogen activator inhibitor type 1, connective tissue growth factor, collagen III and IV expression. Additionally, shikonin markedly inhibited HFD-induced the decrease of proliferator-activated receptor γ (PPARγ) and matrix metalloproteinases-9 (MMP-9) expression and the increase of tissue inhibitor of metalloproteinases-1 (TIMP-1) expression in liver tissue. This study demonstrates that shikonin ameliorates hepatic lipid dysregulation and fibrosis through PPARγ and MMP-9/TIMP-1 axis, suggesting that shikonin may be a potential therapeutic agent for the treatment of NAFLD.