A major challenge in fish physiology is to understand the mechanisms underlying the transcriptomic responses of fish brain to food deprivation. Differential gene expression analysis identified in total 2240 transcripts that presented >2-fold change (adjusted p < 0.01) between each treatment and the control group (C). The identity of the transcripts was obtained with annotation against multiple public databases and they were grouped according to their expression patterns. The gene ontology terms that were substantially affected were identified by functional annotation analysis. Genes related to ion transport, cell cycle and cell adhesion were mainly regulated during fasting and refeeding. These findings contribute to identify key indicators for the molecular basis of brain functions during periods of starvation in gilthead seabream.