High-affinity excitatory amino acid transporters (EAATs) regulate extracellular glutamate levels. Zebrafish (Danio rerio) provides an excellent model to study the function of different neurotransmitter systems. Although the identification of the EAAT family is well established in the mammalian central nervous system (CNS), EAAT-related genes and their expression profile in zebrafish have not yet been reported. Here we identify and describe the expression profile of EAATs-related genes and functional properties of glutamate uptake in three major brain structures from zebrafish (telencephalon, optic tectum and cerebellum). Searches on zebrafish genome databases and a phylogenetic analysis confirmed the presence of several EAAT-related genes (EAAT2, EAAT3, three EAAT1 paralogs and two EAAT5 sequences). All sequences identified were expressed in the structures analyzed. EAAT2 and EAAT3 were the most prominent glutamate transporters expressed in all brain areas. A uniform expression was observed for EAAT1A, whereas higher EAAT1B transcript levels were detected in telencephalon. Lower amounts of EAAT1C transcripts were observed in cerebellum when compared to other structures. No EAAT4-related sequence was found in the zebrafish genome. The EAAT5A expression was similar to EAAT5B in the telencephalon, while EAAT5B was less expressed than EAAT5A in optic tectum and cerebellum. Moreover, the glutamate uptake was significantly higher in optic tectum, which indicates functional differences within zebrafish brain structures. Altogether, the study of glutamate uptake in zebrafish could be important to evaluate the modulation of glutamatergic signaling through pharmacological and toxicological studies.