In the present study, we aimed to assess the adverse effects of zearalenone (ZEA) at environmentally relevant concentrations (0.5, 1, 5 and 10 μg l ) on hypothalamic-pituitary-gonadal axis associated reproductive function using zebrafish model. ZEA was exposed to female zebrafish for 21 days to assess growth indices such as condition factor, hepatosomatic index, gonadosomatic index and caspase 3 activity. Further, expression of estrogen receptor (ER) α and CYP19a1b genes in the brain, ERα and vitellogenin (Vtg) genes in the liver and follicle-stimulating hormone receptor, luteinizing hormone receptor, ERα, steroidogenic acute regulatory protein, 3β-hydroxysteroid dehydrogenase (HSD), 17-βHSD and CYP19a1 genes in the ovary were also investigated. Our results showed that there were no significant changes in the condition factor and hepatosomatic index, whereas a significant (P < .05) reduction in the gonadosomatic index, increase in caspase 3 activities and Vtg expression was observed at higher concentration. However, no significant changes were observed at lower treatment levels. Further, we also observed significant (P < .05) upregulation in ERα, Vtg, luteinizing hormone receptor, steroidogenic acute regulatory protein, 3β-HSD, 17β-HSD, CYP19a1 and CYP19a1b genes in treatment groups with higher levels of ZEA. Moreover, in histopathological examination, we observed oocyte atresia and oocyte membrane detachment in ovaries at the highest concentration. In conclusion, the present study revealed the negative impact of ZEA on zebrafish reproductive system by involvement of the hypothalamic-pituitary-gonadal axis-associated reproductive function.