Background Cross-talk between mitogen-activated protein kinase and estrogen has been reported; however, the role of BRAF V600E in the estrogen responsiveness of thyroid cancer is unknown. We elucidated the effect of BRAF V600E on the estrogen-induced increase in metastatic potential in thyroid cancer. Methods Using a pair of cell lines, human thyroid cell lines which harbor wild type BRAF gene (Nthy/WT) and Nthy/ BRAF V600E (Nthy/V600E), the expression of estrogen receptors (ERs) and estrogen-induced metastatic phenotypes were evaluated. Susceptibility to ERα- and ERβ-selective agents was evaluated to confirm differential ER expression. ESR expression was analyzed according to BRAF V600E status and age (≤50 years vs. >50 years) using The Cancer Genome Atlas (TCGA) data. Results Estradiol increased the ERα/ERβ expression ratio in Nthy/V600E, whereas the decreased ERα/ERβ expression ratio was found in Nthy/WT. BRAF V600E -mutated cell lines showed a higher E2-induced increase in metastatic potential, including migration, invasion, and anchorage-independent growth compared with Nthy/WT. An ERα antagonist significantly inhibited migration in Nthy/V600E cells, whereas an ERβ agonist was more effective in Nthy/WT. In the BRAF V600E group, ESR1/ESR2 ratio was significantly higher in younger age group (≤50 years) compared with older age group (>50 years) by TCGA data analysis. Conclusion Our data show that BRAF V600E mutation plays a crucial role in the estrogen responsiveness of thyroid cancer by regulating ER expression. Therefore, BRAF V600E might be used as a biomarker when deciding future hormone therapies based on estrogen signaling in thyroid cancer patients.