Abstract Background Systemic inflammation, documented before rheumatoid arthritis (RA) diagnosis, is associated with accelerated atherosclerosis. We aimed to compare the prevalence of carotid plaque (CP) in RA patients in the first five years since diagnosis and healthy controls, and to determine disease characteristics associated with the presence of subclinical atherosclerosis in RA patients. Methods This was a cross-sectional study. We recruited 60 RA patients in the first five years since diagnosis and 60 matched healthy controls. Carotid ultrasound was performed to detect the presence of CP and measure carotidintima media thickness (cIMT). Subclinical atherosclerosis was considered as the presence of CP and/or increased cIMT. Distribution was evaluated with the Kolmogorov-Smirnov test. Comparisons were made with Chi-square or Fisher's exact test for qualitative variables and Student's t or Mann-Whitney's U test for quantitative variables. A p-value < 0.05 was considered significant. Results There were no differences in the demographic characteristics between RA patients and controls. The mean disease duration was 2.66 ± 1.39 years. A higher prevalence of CP (30.0% vs. 11.7%, p = 0.013), bilateral CP (18.3% vs. 3.3%, p = 0.008), increased cIMT (30.0% vs. 6.7%, p = 0.001), and subclinical atherosclerosis (53.3% vs. 18.3%, p = < 0.001) was found in RA patients. RA patients with subclinical atherosclerosis were older (56.70 years vs. 50.00 years, p = 0.002), presented a higher prevalence of dyslipidemia (53.1% vs. 14.3%, p = 0.002), and higher prevalence of classification in moderate-high disease activity category measured by DAS28-CRP (68.8% vs. 35.7%, p = 0.010). The latter variable persisted independently associated with subclinical atherosclerosis in the binary logistic regression (OR 6.11, 95% CI 1.51–24.70, p = 0.011). Conclusions In the first five years since diagnosis, higher prevalence of subclinical atherosclerosis, including CP was found in RA patients. Carotid ultrasound should be considered part of the systematic CVR evaluation of RA at the time of diagnosis.