We assessed sex-related differences in the association of pericardial fat volume (PFV) and obesity measured by body mass index (BMI) with coronary atherosclerotic markers (coronary artery calcium score [CAC], coronary luminal stenosis severity, and coronary plaque) in young patients. Patients (n = 174; age <50 years) with suspected coronary artery disease who underwent 64-slice multidetector computed tomography angiography were enrolled. Females tended to have a younger age and increased BMI, normal coronary arteries (free from luminal stenosis), and increased percentage of absent coronary plaque compared with males. There was a significant independent association between PFV with coronary luminal stenosis and between PFV and BMI with coronary noncalcified plaque presence after adjustment for conventional cardiac risk factors. On the other hand, males showed a more increment in PFV, CAC, percentage of calcified plaque, and percentage of significant coronary luminal stenosis compared with females. There was a significant independent association of PFV with CAC, significant coronary stenosis, and calcified plaque presence, while no association was observed between BMI with coronary markers in young males. In conclusion, PFV, but not BMI, showed a significant independent association with advanced coronary atherosclerosis in young male patients.