Malnutrition is a significant comorbidity in nearly one-third of the 8 million deaths in children under five years of age worldwide. Children with severe acute malnutrition have severely disturbed physiology and metabolism. Considering the vital importance of amino acids and the likely changes with the therapeutic diet, we aimed at evaluating these changes in children with SAM at baseline and after rehabilitation with a therapeutic diet at 14 days. Severe acute malnutrition defined as per WHO, for children between 6 months and 5 years with weight for height/length \ -3SD of WHO charts, bilateral pitting edema, and mid-upper arm circumference (MUAC) \ 1.5 cm. A total of 38 children were enrolled as cases, whereas the control group comprised of 37 children. Anthropometric measurement and estimation of amino acids in the blood were done at the baseline and after dietary rehabilitation. The individual levels of the essential and nonessential amino acids were significantly lower in the cases as compared to the controls, except for Aspartate and Threonine. The levels of amino acids increased significantly after dietary rehabilitation except for arginine, however not to the levels of those in controls. Most of the metabolites were reflective of maladaptation in SAM. Though nutritional rehabilitation of children with SAM improved the levels of amino acids, these levels were still low when compared to the controls, stipulating that complete metabolic recovery may take a longer duration of time. This necessitates the continuation of nutritional rehabilitation for a longer time and regular follow up of these children to ensure better compliance.