Background: Rheumatoid arthritis (RA) is one of the most common autoimmune diseases that result in chronic inflammation of the joints. n-3 polyunsaturated fatty acids (PUFAs) have been suggested to play a role in the pathogenesis and clinical course of RA. The purpose of the present study was to investigate whether erythrocyte levels of n-3 PUFA are associated with an increased risk of RA and whether this could potentially serve as an indicator of RA disease activity in Korean women. Methods: A total of 100 female RA patients and 100 healthy women were enrolled into this study. Erythrocyte fatty acid composition and RA disease activity were evaluated in all patients. Results: Erythrocyte levels of α-linolenic acid (ALA; 18:3n3), eicosapentaenoic acid (EPA; 20:5n3), and the omega-3 index [EPA + docosahexaenoic acid (DHA)] were significantly lower in RA patients than in healthy controls. Multivariable-adjusted regression analysis showed that the levels of ALA, EPA, and the ratio of EPA to arachidonic acid were negatively associated with the risk of RA after adjusting for body weight and smoking status. Additionally, the concentration of prostaglandin E₂ was significantly decreased with increased levels of erythrocyte DHA among RA patients. Conclusions: Erythrocyte levels of EPA and ALA were negatively associated with the risk of RA in Korean women, which may be related to eicosanoid metabolism.