The role of gold nanoparticles (AuNPs) in the treatment of autoimmune diseases remains mysterious. Therefore, we investigated the effect of AuNPs on collagen-induced arthritis (CIA) and the impact of particle size on the tissue distribution of AuNPs. CIA model was set up in Wistar rats using bovine collagen type ІІ. CIA rats were then divided into five groups: CIA model (positive control), AuNPs treated- (sphere shape with size: 5, 25, and 75 nm), and methotrexate (MTX)-treated-rats. Untreated rats were run in parallel as normal control. At the end of the experiment, the radiographic assessment was done. Histopathological changes in the joints and vital organs were investigated. Liver- [aspartate transaminase (AST) and alanine transaminase (ALT)] and kidney- (creatinine) functions were measured. The gold bio-accumulation was measured quantitatively with inductively coupled plasma mass spectrometry (ICP-MS). Histopathological results revealed that AuNPs reduced the severity of arthritic symptoms in CIA rats. No histological changes were detected in vital organs. Importantly, AuNPs were deposited in all the examined organs, and the accumulation was size-dependent, with 75 nm demonstrated the least distributed one. Our results revealed that AuNPs decreased both liver and kidney functions as compared to normal controls. In conclusion, our data shed light on the therapeutic efficacy of AuNPs in experimental rheumatoid arthritis compared with a choice size (25 nm). Further investigations to investigate the immunological changes associated with AuNPs are in process.