Rheumatoid arthritis (RA) remains a therapeutic challenge because of the suboptimal efficacy and significant adverse effects of current treatments. Obakulactone (OL), a natural tetracyclic triterpenoid isolated from Phellodendri cortex, has emerged as a promising candidate for RA intervention. However, its underlying mechanism remains poorly understood. In this study, we investigated the therapeutic effects of OL and its molecular mechanisms in RA using a multifaceted approach. A complete Freund’s adjuvant (CFA)-induced RA rat model revealed that OL significantly alleviated joint swelling and restored the expression of CD3⁺ T cells and CD68⁺ macrophages in joints, and the polarization state of macrophages shifted from proinflammatory M1 (CD86) to anti-inflammatory M2 (CD206) dominant. In addition, OL alleviated pathological changes in lymphoid organs (thymus and spleen), effectively inhibited the differentiation of CD4⁺ T cells into T helper 17 (Th17) cells, and normalized serum levels of inflammatory cytokines (e.g., interleukin (IL)-6 and tumor necrosis factor-α (TNF-α)) and RA diagnostic markers (e.g., c-reactive protein (CRP) and rheumatoid factor (RF)). Multiomics profiling revealed that OL corrected the dysregulated biosynthesis and metabolism of unsaturated fatty acids (e.g., arachidonic acid and linolenic acid) in RA rats, with acyl coenzyme A (CoA) thioesterase 1 (ACOT1) identified as a critical regulator. In vitro studies have shown that OL significantly inhibits cell proliferation and inflammatory cytokine secretion and promotes the apoptosis of RA synovial fibroblasts (SFs). It inhibited the M1 polarization of Raw264.7 macrophages and promoted M2 polarization. Mechanistically, cellular thermal shift assays (CETSA), microscale thermophoresis (MST), surface plasmon resonance (SPR), and short hairpin RNA (shRNA) experiments revealed ACOT1 as the direct target of OL. OL enhanced ACOT1 ubiquitination-mediated proteasomal degradation, thereby reducing downstream stearoyl-CoA desaturase-1 expression and inhibiting the Janus kinase (JAK)–signal transducer and activator of transcription (STAT) and phosphoinositide 3-kinase (PI3K)–protein kinase B (AKT) signaling pathways, thus suppressing inflammation and fibrosis in SFs. This study establishes OL as a potential RA therapeutic agent and highlights ACOT1 as a novel target for RA intervention, offering insights into fatty acid metabolism reprogramming as a therapeutic strategy.