Malnutrition remains an international concern because it represents a major cause of childhood morbidity and mortality. In infants and children malnutrition significant metabolic, hormonal, and immune changes occur with short- and long-term effects and outcomes. Thus, studies which contribute to the prevention, amelioration, or rehabilitation of the detrimental effect of malnutrition are necessary. Investigations on endocrine, metabolic, and immune changes related to severe malnutrition started a long time ago. However, recently there has been little work on these important changes, their mechanism/s of action and interactions, and their effect on different systems. The neuroendocrine system is the initial response to stress, so it is reasonable to assume that this system also plays a key role in the pathophysiological changes during nutritional deprivation. However, many of the newly identified functions/changes are better explained by the action of conventional neurotransmitters (e.g., glutamate and GABA) that constitute a neuronal circuit. In addition, the mechanistic Target of Rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase has emerged as a sensor for nutrients that has a central joint in cellular metabolism, cell growth, and differentiation. Its functions during malnutrition in the central nervous system, endocrine system, and different end organs and tissues (liver, pancreas, muscle, and adipose tissue) need elucidation. This article presents a brief review of neuroendocrine changes during malnutrition and their effects on the modulation of metabolism, growth, and immune functions. The pros and cons of these endocrine changes are discussed as well as their reversibility on nutritional rehabilitation.