Bioaccumulation and biotransformation are critical processes modifying toxicity of easily metabolizable chemicals to aquatic organisms. In this study, tissue-specific accumulation, biotransformation and elimination of a current-use pesticide fipronil in tilapia (Oreochromis niloticus) were quantified by combining in vivo measurements and a newly developed multi-compartmental toxicokinetic model. Waterborne fipronil was taken up via gills and metabolized rapidly and solely to fipronil sulfone. Significant decrease of fipronil residues in liver and intestine during exposure period strongly suggested the induction of metabolism in these two organs. Significant transport of fipronil and fipronil sulfone in the liver-bile-intestine system implied that hepatobiliary excretion and enterohepatic re-absorption played important roles in fipronil metabolism and system circulation of the parent compound and the metabolite. The multi-compartmental model quantitatively described the highly dynamic inter-compartmental transport and rapid branchial clearance of fipronil in fish. Modeling results also suggested that uptake and biotransformation were the stronger driving forces for the inter-compartmental transport of fipronil in fish than the inherent partitioning capacity. Overall, our findings highlight the importance of biotransformation on internal disposition of fipronil in fish, which helps to improve aquatic toxicity assessment of this pesticide.