Perfluoroalkyl acids (PFAAs) have been frequently detected in both the environment and biota, however the endocrine disruption potentials and underlying mechanism of long-chain PFAAs have not yet been fully understood in fish. In the present study, the effects of perfluorodecanoic acid (PFDA) and perfluorotridecanoic acid (PFTrDA) on sex steroid hormones and expression of mRNA of selected genes in hypothalamic–pituitary–gonad (HPG) axis were evaluated after 120d exposure of zebrafish. In addition, production of sex hormones and transcription of steroidogenic genes were measured after in vitro exposure of H295R cells for 48h. Exposure to PFTrDA resulted in reduced production of testosterone (T) along with lesser expression of CYP17A mRNA in H295R cells. In zebrafish, significant up-regulation of vtg1 was observed in males exposed to PFDA, whereas down-regulation was observed in females exposed to PFTrDA. In male zebrafish, concentrations of 17β-estradiol (E2) were significantly increased at 0.01mgL−1 PFTrDA. Significant increases in ratios of E2/T and E2/11-ketotestosterone (11-KT) were observed in male zebrafish after exposure to PFDA or PFTrDA, indicating estrogenic potentials of these compounds. The results of this study showed that long-term exposure to PFDA or PFTrDA could modulate sex steroid hormone production and related gene transcription of the HPG axis in a sex-dependent manner. Consequences of endocrine disruptions in reproduction performances of the fish warrant further investigation.