Resveratrol and quercetin are phytochemicals that are found in a variety of plants. The aim of this study was to investigate the effect of resveratrol and quercetin on epithelial-mesenchymal transition (EMT) of CD133+ and CD133- pancreatic cancer cells. Cancer stem cells (CD133+ cells) were obtained from the PANC-1 cells by the MiniMACS system. CD133+ and CD133- PANC-1 cells were treated with different concentrations (5, 10, 25, 50, and 100 µM) of resveratrol and quercetin. Cell growth and cytotoxicity were evaluated by MTT assay. Anticancer and anti-metastatic properties of resveratrol and quercetin were determined by immunocytochemistry using antibodies (ACTA-2, IL-1β, N-cadherin, TNF-α, and vimentin). The immunostaining intensity of CD133+ cells was stronger than CD133- cells. ACTA-2, IL-1β, and N-cadherin immunoreactivities were significantly decreased, whereas TNF-α and vimentin immunoreactivities significantly increased in quercetin-treated CD133+ cells. Moreover, N-cadherin and TNF-α immunoreactivities significantly decreased in resveratrol-treated CD133+ cells. The reduction in N-cadherin and ACTA-2 immunoreactivities was higher than the increase in vimentin immunoreactivity, quercetin could prevent EMT to a greater extent than resveratrol in pancreatic cancer stem cells because of the reduced expression of N-cadherin. Quercetin could be more effective in inhibiting metastasis compared to resveratrol.