Toll-like receptors are membrane-bound proteins which plays a vital role in the regulation of innate immune response which is involved in various inflammatory disorders. 3,6-Dihydroxyflavone (3,6-DHF) is a known chemo preventive agent which is used in the treatment of various cancers including breast cancer and an effective JNK kinase inhibitor which can efficiently block the TLR2-mediated signaling pathways. In this current study, we have explored inhibition of 3,6-DHF in TLR2/TLR1 heterodimerization. We stimulated HEK cells by Pam 3 CSK 4 which specifically induced inflammation through TLR2/TLR1 binding. Secretion of the inflammatory cytokine in Pam 3 CSK 4 -induced HEK293-hTLR2 cells was considerably reduced by 3,6-DHF, implying that 3,6-DHF inhibited Pam 3 CSK 4 -induced TLR2/TLR1 signaling specifically. In addition, 3,6-DHF did not cause severe cytotoxicity against human embryonic kidney (HEK) cells at high concentration up to 100 μM. The binding affinity of 3,6-DHF to TLR2 and TLR1 was explored with 10 −5 affinity using bio-layer interferometry and molecular docking studies identified the important active site residues that participate in the inhibition of TLR2/TLR1 heterodimerization. Our results showed that 3,6-DHF inhibits TLR2-mediated inflammatory signaling by direct binding and the insights in designing more potent drug candidates by targeting the interacting crucial active site residues in TLR2/TLR1.