Background Rheumatoid arthritis (RA) is a progressive, symmetric, and erosive polyarthritis with a variety of extraarticular manifestations such as mononeuritis multiplex, central nervous system vasculitis, Felty's syndrome, dyslipidemia, carditis, and interstitial lung disease. Vitamin D plays a role in both adaptive and innate immunity, and its deficiency leads to the development of many autoimmune disorders. Additionally, RA patients have a lipid paradox consisting particularly of dysfunctional and low levels of high-density lipoprotein (HDL) with reduced low-density lipoprotein lowering effect, which increases cardiovascular morbidity and potentiates widespread systemic inflammation. Both are modifiable risk factors. Although there are numerous studies on vitamin D and HDL cholesterol in disease progression in RA, there is sparse literature from India studying both these factors in combination. In this study, we tried to establish the correlation of serum vitamin D and HDL cholesterol levels, if any, with disease activity using the Disease Activity Score 28 Erythrocyte Sedimentation Rate (DAS28 ESR) score. Methods A descriptive cross-sectional study comprising 80 patients was conducted at a tertiary care center in Eastern India over 12 months. Newly diagnosed RA patients aged >17 years satisfying the diagnostic criteria were included. Serum vitamin D level and HDL cholesterol were measured. Then, the DAS28 ESR score was calculated, and a correlation was looked for between serum vitamin D and HDL cholesterol. Results Patients aged 35-43 years accounted for 32 (42.5%) of participants, of whom 58 (72.5%) were females. Almost half, 38 (47.5%), had vitamin D deficiency. The mean vitamin D level was 22.988 ± 10.01 ng/ml. The mean HDL cholesterol level was 42.3 ± 7.23 mg/dl. The mean DAS28-ESR score was 3.81 ± 1.19. A statistically significant inverse correlation was found between vitamin D levels and DAS28 ESR score (p -0.0003) and HDL (p -0.000349). Conclusions Vitamin D deficiency and low HDL cholesterol levels are more common in RA patients. These factors may contribute to increased disease activity. Both are treatable factors in addition to conventional therapies.