Abstract This study was conducted to investigate the anti-inflammatory activity of Polygala molluginifolia (Polygalaceae) on the mouse pleurisy model induced by carrageenan. P. molluginifolia is a plant native to southern Brazil that is popularly called “canfora”. The Polygala genus is used to treat different pathologies, including inflammatory diseases, in traditional medicine. Material and methods The whole P. molluginifolia plant material was extracted by maceration with 96% ethanol. The crude hydroalcoholic extract (CE) was subjected to chromatographic procedures to produce various derivate fractions, including its aqueous (Aq), ethyl acetate (EtOAc), and hexane (Hex) fractions. Compound 1 (5,3′,4′-trihydroxy-6″,6″-dimethylpyrano [2″,3″:7,6] isoflavone) (Iso), which was isolated from the EtOAc fraction, and Compound 2 (rutin) (Rut), which was isolated from the Aq fraction, were identified using 1H and 13C NMR spectroscopy and quantified using an HPLC apparatus. Results The CE, the Aq, EtOAc, and Hex fractions, and the isolated compounds Iso and Rut were able to reduce cell migration and exudation. Furthermore, the plant material also decreased the myeloperoxidase (MPO) and adenosine-deaminase (ADA) activities and the nitric oxide (NOx), tumor necrosis factor-alpha (TNF-α), and interleukin-1 beta (IL-1β) levels. In addition, Iso and Rut reduced the TNF-α and IL-1β mRNA expression levels and significantly decreased NF-κB p65 phosphorylation. Conclusion The results show that P. molluginifolia has a significant anti-inflammatory action and that this effect is due, at least in part, to the presence of Iso and Rut in large amounts. Moreover, this effect was found to be closely related to the inhibitory effects of the isolated compounds on the NF-κB pathway.