Rheumatoid arthritis fibroblast-like synoviocytes (RA-FLSs), a pathological hallmark of rheumatoid arthritis (RA), exhibit the characteristics of tumor cells. The extracts of Cirsium japonicum var. ussuriense have been shown to possess antitumor and anti-inflammatory activities. Our study aimed to investigate the effects of pectolinarin, a flavonoid compound isolated from C. japonicum var. ussuriense, on RA. Cell viability was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide assay. Apoptosis was determined by flow cytometry analysis and Western blot analysis of Bax and Bcl-2 levels. Inflammation was assessed by detecting the expressions and secretion of interleukin (IL)-6 and IL-8 using quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. The production of nitric oxide (NO) and prostaglandin E2 (PGE2) was also measured. The effects of pectolinarin on the phosphatidylinositol 3 kinase (PI3K)/protein kinase B (Akt) pathway were examined by Western blot. We found that pectolinarin significantly inhibited cell viability at 24 and 48 hours in a dose-dependently manner in RA-FLSs. Pectolinarin reduced the apoptotic rate, increased Bax level, and decreased Bcl-2 level in RA-FLSs. Pectolinarin inhibited the messenger RNA expression and secretion of IL-6 and IL-8, as well as the production of PGE2 and NO in RA-FLSs. Furthermore, pectolinarin inactivated the phosphatidylinositol 3 kinase/protein kinase B (PI3K/Akt) pathway in RA-FLSs. Activation of the PI3K/Akt pathway by 740Y-P impaired the effects of pectolinarin on cell viability, apoptosis, and inflammation in RA-FLSs. In conclusion, pectolinarin suppressed cell proliferation and inflammatory response and induced apoptosis in RA-FLSs via inactivation of the PI3K/Akt pathway.