Background: Rheumatoid arthritis (RA) is an autoimmune disease. Bone marrow mesenchymal stem cells (BMSCs) have multilineage differentiation and anti-inflammatory potential, and small interfering RNAs (siRNAs) can inhibit the target gene expression, which make them suitable for ameliorating RA. The current study was aimed to explore the effect and potential mechanisms of siRNAs targeting IL-1β/TNF-α combined with BMSCs transplantation in ameliorating RA in rats. Methods: Collagen-induced arthritis (CIA) model rats were randomly divided into five groups: PBS (Model control group), methotrexate (Positive drug treatment group), BMSCs (BMSCs transplantation group), siRNA (IL-1β/TNF-α siRNAs injection group), siRNA + BMSCs (Both IL-1β/TNF-α siRNAs injection and BMSCs transplantation group). After treatment for 0, 7, 14, 21, 28 days, the ameliorating effect was comprehensively assessed through results of the body weight, toe swelling value, the immobility time of forced swimming, the serum concentrations of IL-1β and TNF-α, knee joint DR-X imaging and pathological analysis as well as of IL-1β, TNF-α and NF-κB mRNA expression in spleen tissue. Furthermore, the potential underlying mechanism involving the NF-κB signaling pathways was also explored. Results: Compared with the PBS group, BMSCs, siRNA, siRNA + BMSCs treatment groups showed significant lower toe swelling value, immobility time, spleen index, serum contents of IL-1β and TNF-α. In addition, the DR-X results showed that the knee carton surface tended to smoothing without bone hyperplasia, suggesting that these three treatments were all able to successfully ameliorate RA symptoms. In addition, compared with the PBS group, the protein expression of p-NF-κB-p65 was significantly reduced in the knees of siRNA + BMSCs rats. BMSCs labeled with BrdU were also found in the knees of rats. Moreover, the mRNA expression of IL-1β, TNF-α and NF-κB-P65 in spleen tissue of siRNA + BMSCs rats were all significantly inhibited. Conclusions: Our results demonstrated for the first time that siRNA + BMSCs was able to ameliorate RA inflammation by inhibiting the activation of NF-κB signaling pathways and reducing the erosion of articular cartilage, and siRNA + BMSCs treatment showed synergism effects in helping ameliorating the inflammation and cartilage repair of RA rats. Therefore, the results of our present study provide a new idea for gene and stem cell therapy for RA.