Non-alcoholic Fatty Liver Disease (NAFLD) is a widespread liver disorder caused by excess fat accumulation in the liver with no significant alcohol consumption. This condition has been linked to the development of cardiovascular diseases (CVD) and atherosclerosis. Carotid intima-media thickness (CIMT) and carotid plaques, which are established markers of subclinical atherosclerosis, were used to assess CVD risk. However, few studies have explored the correlation between NAFLD and subclinical atherosclerosis, especially in young and middle-aged men. A study on 200 male patients aged 18-55 years aimed to investigate the association between NAFLD fibrosis score (NFS) and CIMT, as well as carotid plaque presence. The study, conducted between July 2023 and January 2024, included CIMT measurements and plaque assessments performed using B-mode ultrasound. Participants were divided into two groups based on CIMT values and plaque presence, and NFS was analyzed for its association with CIMT and plaque. Participants with higher CIMT values had a significantly higher NFS (-2.9 ± 1.13 vs. -1.9 ± 1.4, P < 0.001) than those with lower CIMT values. Similarly, participants with carotid plaque also exhibited a higher NFS (-2.5 ± 1.3 vs. -1.7 ± 1.4, P = 0.002). Multivariate logistic regression analysis showed that NFS was a strong predictor of both increased CIMT (odds ratio [OR]: 1.564%95 CI 1.035-2.363; P = 0.034) and carotid plaque presence (OR: 1.605%95 CI 1.118-2.290; P = 0.010). These results emphasize the potential role of NFS as a marker of subclinical atherosclerosis in young and middle-aged men.