Objective: Chemotherapy is still the most common and primary treatment option for treating pancreatic cancers because metastasis has already occurred at the time of diagnosis, difficulties of the operation due to its location, and lack of targeted treatment approaches. Moreover, the high chemoteuropatic resistance seen in pancreatic cancer makes research on alternative drug treatments mandatory. Juglone, a natural naphthaquinone found in members of the Juglandaceae family, has various pharmacological effects such as antiviral and antibacterial. It has also been shown to be an effective cytotoxic agent through the production of reactive oxygen species in studies conducted with cancer cell lines. Remarkably, selenium, an important trace element of the cell, was shown to inhibit metastasis, strengthen cell-cell attachments, and reduce angiogenesis. Based on these data, we investigated the effects of juglone-selenium (J/S) combination on epithelial-mesenchymal transition (EMT) and migration in PANC-1 and BxPC-3 cells. Methods: The effects of juglone application in the presence of 2,5 µM NaSe at 5, 10, 15 and 20 µM concentrations on the expression of FOXL1, VIM, and MMP-7 genes were determined by qPCR. In addition, the effects of J/S on the migration features of cancer cells were monitored by wound healing tests. Results: According to qPCR results, J/S application showed different effects on FOXL1, VIM, and MMP-7 gene expressions, which are critical for EMT, in both cell lines. According to the wound healing assay results, the migration of cancer cells was suppressed in both cell lines compared with the control group. Conclusion: Consequently, our studies have supported that juglone can be an effective therapeutic agent on pancreatic cancer, and our findings also suggest that selenium can strengthen these anticancer effects of juglone.