Atherosclerosis, a leading cause of mortality and morbidity worldwide, involves inflammatory processes that result in plaque formation and calcification. The early detection of the molecular changes underlying these processes is crucial for effective disease management. This study utilized positron emission tomography/computed tomography (PET/CT) with [18F] sodium fluoride (NaF) as a tracer to visualize active calcification and inflammation at the molecular level. Our aim was to investigate the association between cardiovascular risk factors and [18F] NaF uptake in the left and right common carotid arteries (LCC and RCC). A cohort of 102 subjects, comprising both at-risk individuals and healthy controls, underwent [18F] NaF PET/CT imaging. The results revealed significant correlations between [18F] NaF uptake and cardiovascular risk factors such as age (β = 0.005, 95% CI 0.003–0.008, p < 0.01 in LCC and β = 0.006, 95% CI 0.004–0.009, p < 0.01 in RCC), male gender (β = −0.08, 95% CI −0.173–−0.002, p = 0.04 in LCC and β = −0.13, 95% CI −0.21–−0.06, p < 0.01 in RCC), BMI (β = 0.02, 95% CI 0.01–0.03, p < 0.01 in LCC and β = 0.02, 95% CI 0.01–0.03, p < 0.01 in RCC), fibrinogen (β = 0.006, 95% CI 0.0009–0.01, p = 0.02 in LCC and β = 0.005, 95% CI 0.001–0.01, p = 0.01), HDL cholesterol (β = 0.13, 95% CI 0.04–0.21, p < 0.01 in RCC only), and CRP (β = −0.01, 95% CI −0.02–0.001, p = 0.03 in RCC only). Subjects at risk showed a higher [18F] NaF uptake compared to healthy controls (one-way ANOVA; p = 0.02 in LCC and p = 0.04 in RCC), and uptake increased with estimated cardiovascular risk (one-way ANOVA, p < 0.01 in LCC only). These findings underscore the potential of [18F] NaF PET/CT as a sensitive tool for the early detection of atherosclerotic plaque, assessment of cardiovascular risk, and monitoring of disease progression. Further research is needed to validate the technique’s predictive value and its potential impact on clinical outcomes.