Background: The risk of essential amino acid deficiency (EAAD), like lysine in cereal-based diets, can impact growth in young children. Lysine being the first limiting amino acid in cereal-based diets, is also associated with stunting. Developing a non-invasive urinary based metabolomic profiling for quick screening of EAAD in stunted children can be useful to design targeted nutritional therapies. Methods: A parallel group interventional trial of lysine supplementation (80 mg/kg/day in an orange flavored drink) was conducted in stunted (height-for-age Z-score <-2SD, n=24) 6-11 years, South Indian children to evaluate urinary biomarkers for EAAD, in comparison with control non-stunted children (n=27) who received an orange flavored placebo drink for 3-months. At baseline and monthly intervals, clinical examinations, height, weight, circumferences (cranial, forearm, upper-arm, waist), skin folds, muscle strength, food intake-recalls were measured, along with urine and blood sampling at baseline and endline. The urine metabolome was analyzed by Q-Exactive orbitrap-based mass spectrometer using Compound Discoverer software (Thermo Scientific). Differences in anthropometry were analyzed by ttest and repeated measures models. Result: Anthropometric measurements were significantly different (p<0.038) at baseline between groups (p<0.0077). Preliminary urinary metabolomic profiles showed a difference between groups in lysine-related metabolites at baseline and alterations with lysine intervention. Metabolites of tryptophan degradation and utilization, threonine, methionine, cysteine, and branched chain amino acid biosynthesis pathways were altered at baseline between groups and with lysine intervention. The metabolites gly-leu, kynurenic acid, 6-oxo-pipecolinic acid, dimethylhistidine and pyridoxamine were found to be downregulated and 2-oxobutyric acid and 7-ketodeoxycholic acid were found to be upregulated that are linked with protein metabolism pathways specifically lysine degradation and can be used as non-invasive biomarkers of lysine sufficiency state in stunted children. Conclusion: Urinary metabolomic profiles showed a difference between groups in lysine-related metabolites at baseline and alterations with lysine intervention in various metabolites that can be used for screening the growth faltering at early stages towards designing targeted nutritional therapies. A validation of urine metabolomic profiles using the blood metabolomic profiles could provide more insights towards designing targeted nutritional therapies.