Introduction: Undernutrition in vulnerable children under the age of 5 is one of the widespread challenges in pediatric gastroenterology, which can be affected by a common environmental risk factor known as gut microbiota. Dysbiosis of gut microbiota has a significant link with the development of metabolic instability and alteration of energy intake. This review investigated the efficacy of probiotic and prebiotic administration on impaired microbial interactions to control the adverse clinical and physical status of undernourished children. Material and Methods: A wide range of human and animal trials conducted between 2000-2022 were searched in Google Scholar and PubMed electronic databases. Related English articles were selected using the keywords “undernutrition”, “wasting”, “stunting”, “underweight”, “probiotic”, and “prebiotic”. Results: Physiologically, most of the converging evidences support the positive effect of probiotic and prebiotic supplements in improving the balance of gut microbiota, immune and hormonal responses, host metabolic pathways. Moreover, a positive correlation has been reported between supplement consumption and the increase in height, weight, waist circumference, and body mass index of children. Various Lactobacillus and Bifidobacterium strains and galactoligosaccharide and fructo-oligosaccharide prebiotics were commonly studied supplements that have even shown a significant synergistic effect. Conclusion: Microbiome-based pharmaceutical interventions by modifying anthropometric characteristics and physiological axes are promising choices for the management of childhood malnutrition. The design of diverse pro- and prebiotic combinations with optimal dose balance is a requirement for the potential progression of this microbial therapeutic method. Keywords: Childhood undernutrition, Probiotic, Prebiotic, Dysbiosis