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This study was carried out to assess the effect of fasting and feeding on growth, intestinal morphology and density of cholecystokinin (CCK‐) and neuropeptide Y (NPY‐) immunoreactive cells in Rhamdia quelen. Fish were fed during 30 days with three commercial feeds containing different protein levels (T1 = 25%, T2 = 30% and T3 = 45%) while one group remained food deprived (T0). Our results show that the T3 group presented higher final mean weight and specific growth rate, while food‐deprived group showed a significant weight loss. Histological analyses showed that the epithelial area of the intestine was significantly affected by fasting. Also, immunohistochemical analyses showed changes in enteroendocrine cells density, according to nutritional status. Cholecystokinin cell density was higher in T2 and T3 groups, while no differences in NPY cell density were observed between fed groups. Neuropeptide Y and CCK cell densities decreased in fasted group. Nevertheless, this group presented a higher NPY:CCK cell ratio (5:1) compared to fed groups (1–1.5:1), suggesting NPY acts as a peripheral orexigenic factor. These results show that the structure and endocrine functions of R. quelen intestine respond with a downregulation mechanism to endure long‐term starvation.