Rheumatoid arthritis (RA) patients are more likely to develop cardiovascular disease (CVD), which increases the risk of morbidity and mortality. Periodontitis is known to be associated with CVD, yet its relationship with CVD in RA is limited. Aim of the work: To examine the relationship between periodontitis with subclinical atherosclerosis and with long term CVD risk. Examining if periodontitis treatment can be associated with CVD improvement was well thought out. Patients and methods: This prospective interventional study included 49 adults with RA. Demographic, clinical and therapeutic data and laboratory markers were assessed. Dental examination for periodontitis was performed. The carotid intima media thickness (CIMT) and Framingham risk score (FRS) were evaluated. Medical treatment was provided to RA patients with periodontitis, and assessments were repeated after 6 months. Results: The mean age of the patients was 46.4 ± 12.4 years, disease duration 10.9 ± 5.4 years and 79.6% were females. 25 (51%) patients had subclinical atherosclerosis, 30 (61.2%) had periodontitis and 25 (51%) had both. RA patients with subclinical atherosclerosis had higher clinical attachment loss (CAL) (3.12 ± 1.45) and higher probing depth (PD) (4.96 ± 1.37) compared to those without (p < 0.001). CAL (b = 0.01, 95 %CI: 0–0.01, p < 0.001), and PD (b = 0.01, 95% CI: 0–0.01; p < 0.001) were independently associated with CIMT. The 30 patients after treatment of periodontitis showed an average improvement in the mean CIMT (0.14 mm, p < 0.001). Conclusion: Periodontitis is associated with subclinical atherosclerosis in RA. Treatment of periodontitis could improve the cardiovascular health in RA patients and prompts physicians to early diagnose and treat periodontitis.