Low temperatures provoke drastic reductions in gilthead sea bream (Sparus aurata) activity and nourishment, leading to growth arrest and a halt in production. However, scarce data exist concerning the implications of central core control during the cold season. The aim of this work was to study the effects of low temperature and recovery from such exposure on the pituitary activity of sea bream juveniles fed 18% or 14% dietary lipid. A controlled indoor trial was performed to simulate natural temperature fluctuation (22 °C to 14 °C to 22 °C). Meanwhile, we determined the regulatory role of the pituitary by analyzing the gene expression of some pituitary hormones and hormone receptors via qPCR, as well as plasma levels of thyroidal hormones. In response to higher dietary lipids, hormone pituitary expressions were up-regulated. Induced low temperatures and lower ingesta modulated pituitary function up-regulating GH and TSH and thyroid and glucocorticoid receptors. All these findings demonstrate the capacity of the pituitary to recognize both external conditions and to modulate its response accordingly. However, growth, peripheral tissues and metabolism were not linked or connected to pituitary function at low temperatures, which opens an interesting field of study to interpret the hypothalamus–pituitary–target axis during temperature fluctuations in fish.