The Mexican pike silverside (Chirostoma estor) is a zooplanktivorous, agastric short-intestined species, and it has been found that increased-frequency feeding (twelve feedings a day) improved feed efficiency and promoted growth by 70%. This work determined the effect of different juvenile feeding frequencies upon the C. estor liver transcriptome. The level of the expression of appetite-regulating peptides was analyzed in silico to understand the mechanisms involved in appetite control in this species. Differential expression analysis showed that up-regulated genes between treatments were related to metabolism, digestive processes, immune system response, apoptosis, growth, and oxidative stress. This information explains the better performance of pike silverside fed 12 times daily. Appetite regulatory peptides were identified for the first time in the liver of C. estor in response to high feeding frequencies, contributing to the general knowledge of the roles of each family of neuropeptides in this agastric, short-intestined fish. The information presented here emphasizes the need to explore further the complex physiological processes involved in appetite regulation in C. estor. Additionally, it will serve as a basis for more specific targeted studies of appetite control to elucidate the mechanisms behind this process.