Quercetin is a flavonoid with a wide range of pharmacological activities, including anticancer, antioxidant, and anti-inflammatory effects. Since it is a nutrient that can be consumed with a regular diet, quercetin has recently garnered interest. Quercetin acts as a phytochemical ligand for the aryl hydrocarbon receptor (AhR). Cleft lip and palate are among the most frequently diagnosed congenital diseases, and exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) during pregnancy induces cleft palate via AhR. In this study, we investigated the preventive effect of quercetin intake on the TCDD-induced cleft palate and its mechanism of action. The in vivo results suggest that quercetin intake by pregnant mice can prevent cleft palate in fetal mice. In vitro, the addition of TCDD induced a reduction in cell migration and the proliferation of mouse embryonic palatal mesenchymal cells, which was mitigated by the addition of quercetin. The addition of quercetin did not alter the mRNA expression levels of the AhR repressor but significantly suppressed mRNA expression of CYP1A1. In addition, the binding of AhR to a xenobiotic responsive element was inhibited by quercetin, based on a chemically activated luciferase expression assay. In conclusion, our results suggest that quercetin reduces the development of TCDD-induced cleft palate by inhibiting CYP1A1 through AhR.