This study aimed to determine the effects of Enrofloxacin (ENR) exposure and depuration on the disruption of thyroid function and growth of juvenile grass carp (Ctenopharyngodon idella) as well as to assess the risk of ENR exposure to human health. Juvenile grass carp were treated with ENR solutions at different concentration gradients for 21 days and then depurated for 14 days. The results indicated ENR accumulation in the juvenile grass carp muscles, which persisted after depuration. In addition, exposure to ENR could alter growth by regulating the expression of genes associated with growth hormone/insulin-like growth factor (GH)/IGF) axis and the hypothalamic-pituitary-thyroid (HPT) axis. During ENR exposure, no significant changes in growth hormone levels were observed; however, a significant increase in the growth hormone level was noted. GH/IGF axis-related genes were upregulated after ENR exposure, and their expression levels remained high after depuration. Notably, a significant increase in the serum triiodothyronine (T3) and thyroxine (T4) levels coincided with the upregulation of HPT axis-related genes in both exposure and depuration treatments, and their expression levels remained high after depuration. Therefore, juvenile grass carp exposure to ENR induces physiological stress through HPT and GH/IGF axes that cannot be recovered after depuration. ENR accumulates in the muscles of juvenile grass carp and may pose a threat to human health. Therefore, exposure of juvenile grass carp to ENR results in impaired thyroid function and impaired growth. In addition, consumption of ENR-exposed fish poses human health risks.