The thyroid axis is a major regulator of metabolism and energy homeostasis in vertebrates. There is conclusive evidence in mammals for the involvement of the thyroid axis in food intake, but in fish, this link is inconclusive. In order to assess the effects of nutritional status on the thyroid axis in goldfish, Carassius auratus, we examined brain and peripheral transcript expressions of genes associated with the thyroid axis [thyrotropin-releasing hormone (TRH), thyrotropin-releasing hormone receptors (TRH-R type 1 and 2), thyroid stimulating hormone (TSH), deiodinase enzymes (DIO2, DIO3) and UDP-glucoronsyltransferase (UGT)] and appetite regulators [Neuropeptide Y (NPY), proopiomelanocortin (POMC), agouti-related peptide (POMC) and cholecystokinin (CCK)] in fasted and overfed fish for 7 and 14 day periods. We show that there was a strong response of the thyroid axis to overfeeding, with an increase of brain TRH and TSHβ expressions after 14 days. In fasted fish, hepatic DIO3 and UGT transcripts were down-regulated from 7 to 14 days, suggesting an increase in thyroid hormone degradation. Nutritional status had no effect on circulating levels of thyroid hormone. Central appetite-regulating peptides exhibited temporal changes in expression, with decreased expression of the appetite-inhibiting peptide POMC, and increased expression of the appetite-stimulating peptide AgRP, from 7 to 14 days for both fasted and overfed fish, with no change in NPY. Intestinal CCK expression was elevated in fasted compared to overfed fish, in contrast to the typical anorexigenic role of this peptide. These results indicate that nutritional status time-dependently affects the thyroid axis. Our study helps to fill a knowledge gap in current fish endocrinological research on the effects of energy balance on thyroid metabolism and function.