Rheumatoid arthritis (RA) is an autoimmune disease characterized by aggressive cartilage and bone erosion. This work aimed to evaluate the metabolomic profile of Medicago sativa L. (MS) seeds and explore its therapeutic impact against RA in rats. Arthritis was induced by complete Freund’s adjuvant (CFA) and its severity was assessed by the arthritis index. Treatment with MS seeds butanol fraction and interlukin‐1 receptor antagonist (IL‐1RA) were evaluated through measuring interlukin‐1 receptor (IL‐1R) type 1 gene expression, interlukin‐1 beta (IL‐1β), oxidative stress markers, C‐reactive protein (CRP), tumor necrosis factor‐alpha (TNF‐α), prostaglandin E2 (PGE2), caspase‐3 (Cas‐3), intracellular adhesion molecule‐1 (ICAM‐1), DNA fragmentation, and chromosomal damage. Total phenolics/ flavonoids content in the ethyl acetate, butanol fraction and crude extract of MS seeds were estimated. The major identified compounds were Quercetin, Trans‐taxifolin, gallic acid, 7,4'‐Dihydroxyflavone, Cinnamic acid, Kudzusaponin SA4, Isorhamnetin 3‐O‐beta‐D‐2'',3'',4''‐triacetylglucopyranoside, Apigenin, 5,7,4'‐Trihydroxy‐3'‐methoxyflavone, Desmethylxanthohumol, Pantothenic acid, Soyasapogenol E, Malvidin, Helilandin B, Stigmasterol, and Wairol. Treatment with MS seeds butanol fraction and IL‐1RA enhanced all the biochemical parameters and the histopathological features of the ankle joint. In conclusion, Trans‐taxifolin was isolated for the first time from the genus Medicago. MS butanol fraction seeds extract and IL‐1 RA were considered as anti‐rheumatic agents.