•Glucose homeostasis is rearranged by dexamethasone (DEX) treatment with long-term deleterious effects.•DEX significantly reduced circulating levels of endogenous cortisol as well as hematocrit.•DEX significantly upregulates gene expression of brain trh along with hypophyseal pomcb and gh.•In contrast to control or cortisol groups, DEX does not promote anion-absorptive currents in the distal intestine.•Only DEX treatment promoted significant differences between proximal and distal intestinal regions’ transepithelial electric resistance. This study approached the long-term oral administration of cortisol (F) and dexamethasone (DEX), two synthetic glucocorticoids, compared to a control group (CT) in the juveniles of a marine teleost, the gilthead seabream (Sparus aurata). Physiologically, DEX treatment impaired growth, which appears to be linked to carbohydrate allocation in muscle and liver, hepatic triglycerides depletion, and reduced hematocrit. Hypophyseal gh mRNA expression was 2-fold higher in DEX than in CT or F groups. Similarly, hypothalamic trh and hypophyseal pomcb followed this pattern. Plasma cortisol levels were significantly lower in DEX than in CT, while F presented intermediate levels. In the posterior intestine, measured short circuit-current (Isc) was more anion absorptive in CT and F compared to the DEX group, whereas Isc remained unaffected in the anterior intestine. The derived transepithelial electric resistance (TEER) significantly differed between intestinal regions in the DEX group. These results provide new insights to understand better potential targeted biomarkers indicative of the differential glucocorticoid or mineralocorticoid-receptors activation in fish.