Toll-like receptor (TLR)-mediated signaling induces cell migration or invasion in several tumors and various stages of cancer. Interactions of mesothelin, a 40-kDa cell surface glycoprotein, with cancer antigen 125 (CA125) is associated with drug resistance, metastasis, and poor clinical outcome of ovarian cancer patients. In this study, we examined the role of TLR5 and TLR7 in the metastasis of ovarian cancer through the induction of mesothelin/CA125 expression and investigated its underlying mechanism. TLR5 agonist (flagellin) and TLR7 agonist (imiquimod) upregulated mesenchymal phenotypes and produced epithelial-mesenchymal transition (EMT)-related cytokines in the SKOV3 cells; however, TLR7 expressing CaOV3 cells had no response to the specific ligand, imiquimod, for enhancing its EMT processes. Stimulation of the SKOV3 cells with flagellin or imiquimod activated Wiskott-Aldrich syndrome protein verprolin-homologous 3 (WAVE3) and mesothelin/CA125, whereas it suppressed the expression of TAp63. Moreover, knockdown of TLR5 or TLR7 in SKOV3 cells profoundly impaired the TLR5- or TLR7-intiated downstream signaling pathway. Loss of WAVE3 in SKOV3 cells led to the inhibition of invasion, suppression of mesenchymal characteristics, prevention of OCT4/SOX2 secretion, and attenuation of mesothelin/CA125 expression after stimulation with flagellin or imiquimod. Although the disruption of mesothelin decreased the migratory activity of the TLR5/7-activated SKOV3 cells, knockdown of mesothelin failed to reduce the expression of mesenchymal markers, OCT4, and SOX2. In addition, targeting OCT4 or SOX2 with siRNA had no effect on the expression of mesothelin and the suppression of transcriptionally active p63 (TAp63) in the TLR5/7-stimulated SKOV3 cells. Our results suggest that TLR5/7-mediated WAVE3 activation not only controls the mesothelin-related EMT processes but also modulates OCT4/SOX2-mediated mesenchymal marker expression. Taken together, both TLR5 and TLR7 expression are critical for the TLR5/7-induced metastasis of ovarian cancer and the inhibition of WAVE3 might be a new therapeutic target to control ovarian cancer metastasis.