Previous studies have indicated that fluoride could induce the damage of thyroid. However, the effects of sesamin on thyroid endocrine function in zebrafish exposed to fluoride have not been clarified. This study was designed to investigate the alleviating effects of sesamin on thyroid endocrine disruption in zebrafish induced by fluoride. The results showed that sesamin significantly improved growth performance in adults exposed to fluoride; decreased significantly the mortality rate, increased remarkably the hatching rate and body length, and alleviated the phenomenon of spinal curvature, yolk cyst and pericardial cyst to varying degrees in fluoride-exposed embryos and larvae. Sesamin alleviated remarkably the damage of thyroid tissues in fluoride-exposed adults. Moreover, sesamin obviously reduced oxidative stress and improved the imbalance of thyroid hormones in fluoride-exposed adults or larvae. In addition, sesamin reversed the expression of endocrine-related genes of thyroid in fluoride-exposed adults or larvae. This indicates that sesamin can affects the thyroid tissue structure, hormone levels, and the expression of endocrine-related genes of thyroid, thus alleviating the thyroid endocrine disorder induced by fluoride and improving the growth and development. This study also demonstrates that sesamin can be a promising novel treatment for thyroid endocrine disorder caused by fluoride.