Background Human periodontal ligament fibroblasts (HPDLFs) represent the first line of defense against pathogens in the periodontal tissue. Porphyromonas gingivialis (P. gingivalis) has been known to be most strongly associated with periodontitis. MicroRNA (miR)-146a is involved in the inflammatory regulation of periodontitis. However, the regulatory mechanism of miR-146a on in P. gingivalis-induced inflammation response in HPDLFs was still unclear. The aim of this study was to investigate whether miR-146a plays a key role in P. gingvalis-induced inflammation responses through regulation of TRAF6 in HPDLFs. Methods MiR-146a expression was measured by real-time polymerase chain reaction (PCR) in HPDLFs stimulated with P. gingivalis and its lipopolysaccharide (LPS). IL-1 ss, IL-6, and IL-8 were determined by enzyme-linked immunosorbent assay (ELISA) in the culture supernatants of HPDLFs after transfected with miR-146a mimic or inhibitor. Meanwhile, the expression of TRAF6 was measured by real-time PCR and Western blot. Then, we used luciferase reporter assay to detect whether miR-146a binds to the 3 '-UTR of TRAF6. By using small interfering RNA (siRNA) of TRAF6, the phosphorylation of p38 mitogen-activated protein kinase (MAPK) was measured by Western blot. Finally, after inhibition of TRAF6 and p38 in HPDLFs, we analyzed the expression of miR-146a upon P. gingivalis challenge. Results P. gingivalis and its LPS significantly induced miR-146a expression in HPDLFs. Overexpression of miR-146a significantly suppressed the IL-1 ss, IL-6 and IL-8 secretion, TRAF6 expression, and p38 phosphorylation. In contrast, the levels of these indexes significantly increased by inhibition of miR-146a. Furthermore, MiR-146a directly binds to the 3 '-UTR of TRAF6 in P. gingivalis-induced HPDLFs, but not in P. gingivalis LPS stimulation. Suppression of TRAF6 could inhibit the phosphorylation of p38. Finally, inhibition of TRAF6 and p38 significantly abolished P. gingivalis-induced miR-146a upregulation in HPDLFs. Conclusions MiR-146a contribute to negative regulation of P. gingivalis-induced proinflammatory cytokines secretion in HPDLFs though TRAF6/p38 MAPK pathway. Maintaining miR-146a homeostasis plays a key role in controlling inflammatory response in periodontal tissues.