Chlorfenapyr is widely used as an insecticide/miticide. Tralopyril, the active metabolite of chlorfenapyr, is used as an antifouling biocide in antifouling systems, and negatively affects aquatic environments. However, it is unclear whether tralopyril is a metabolite of chlorfenapyr in aquatic vertebrates, and there is little data on the bioaccumulation and toxicity of chlorfenapyr to aquatic vertebrates. In this study, the bioaccumulation and elimination of chlorfenapyr in zebrafish were assessed, and tralopyril, the active metabolite of chlorfenapyr, was determined. The effects of chronic exposure to chlorfenapyr on zebrafish liver and brain oxidative damage, apoptosis, immune response, and metabolome were investigated. These results showed that chlorfenapyr has a high bioaccumulation in zebrafish, with bioaccumulation factors of 864.6 and 1321.9 after exposure to 1.0 and 10 μg/L chlorfenapyr for 21 days, respectively. Chlorfenapyr at these concentrations also rapidly accumulated in zebrafish, reaching 615.5 and 10336 μg/kg on the second and third days of exposure, respectively. Chlorfenapyr was degraded to tralopyril in zebrafish; therefore, both chlorfenapyr and tralopyril should be considered when evaluating the risk of chlorfenapyr to aquatic organisms. In addition, chronic exposure caused oxidative damage, apoptosis, and immune disorders in zebrafish liver. Chronic exposure also altered the levels of endogenous metabolites in liver and brain. After 9 days of depuration, some indicators of oxidative damage, apoptosis, and immunity returned to normal levels, but the concentration of endogenous metabolites in zebrafish liver was still altered. Overall, these results provide useful information for evaluating the toxicity and environmental fate of chlorfenapyr in aquatic vertebrates.