Neuropeptide Y (NPY) is an evolutionarily conserved neuropeptide implicated in feeding regulation in vertebrates. In mammals, NPY neurons coexpress Agouti-related protein (AgRP) in the arcuate nucleus of the hypothalamus, and NPY/AgRP neurons activate orexigenic signaling to increase food intake. Zebrafish express npy and two agrp genes, agrp1 and agrp2, in the brain. Similar to mammals, NPY and AgRP1 act as orexigenic factors in zebrafish, but the exact distribution of NPY and AgRP neurons in the zebrafish brain and the regulation of these genes by metabolic states remain unclear. In this study, we analyzed the tissue distribution of npy, agrp1, and agrp2 mRNA in the brain of larval and adult zebrafish. We detected the expression of agrp1, but not npy, in the hypothalamus of larval zebrafish. In the adult zebrafish brain, npy mRNA expression was detected in the dorsal area of the periventricular and lateral hypothalamus, but fasting induced upregulation of npy only in the lateral hypothalamus, indicating that NPY neurons in this area are implicated in feeding regulation. However, consistent with the findings in larval zebrafish, NPY neurons in the hypothalamus did not coexpress AgRP1. In contrast, fasting resulted in a dramatic increase in AgRP1 neurons in the ventral periventricular hypothalamus, which do not coexpress NPY. In addition, we found for the first time that npy- and agrp1-expressing neurons function as GABAergic inhibitory neurons in zebrafish, as they do in mammals. Taken together, our results show that the zebrafish NPY/AgRP system is involved in appetite regulation. In addition, our data suggest that although npy and agrp1 were initially expressed in distinct neurons, evolution has resulted in their coexpression in mammalian hypothalamic neurons.