The risk of essential amino acid deficiency (EAAD), like lysine in cereal-based diets, can impact growth in young children. Urinary metabolomic biomarkers can be used for rapid non-invasive screening for EAAD in stunted children, and to design targeted nutritional therapies. 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 intakerecalls were measured, along with urine and blood sampling at baseline and end-line. The urine metabolome was analyzed by Q Exactive orbitrap-based mass spectrometer using Compound Discoverer software (Thermo Scientific). Differences in anthropometry were analyzed by t-test and repeated measures models. Anthropometric measurements were significantly different (p<0.038) at baseline and after 3-months (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 urine metabolomic profile with EAAD is different between stunted and nonstunted children at baseline and in response to lysine supplementation. A validation of urine metabolomic profiles using the blood metabolomic profiles could provide more insights towards designing targeted nutritional therapies.