A useful animal model of intestinal injury is pivotal for studying its pathogenesis and developing nutritional interventions (e.g., amino acid supplementation). Here, we propose the use of indomethacin (IDMT) to induce intestinal inflammation in neonatal pigs. Fourteen-day-old piglets fed a milk replacer diet receive intraperitoneal administration of IDMT (5 mg/kg body weight) for 3 consecutive days. On day 4, blood and intestinal samples are obtained for physiological and biochemical analyses. IDMT increases blood DAO activity, I-FABP concentration, neutrophil and eosinophil numbers; intestinal MMP3 mRNA levels, MPO activity, and MDA concentration; but reduces the plasma concentration of citrulline (synthesized exclusively by enterocytes of the small intestine), intestinal GSH-Px activity, and mRNA levels for villin, I-FABP, TRPV6, AQP10, and KCNJ13. Moreover, extensive hemorrhagic spots, thinned intestinal wall, and ulcers in the distal jejunum and ileum are observed in IDMT-challenged piglets. Furthermore, IDMT decreases intestinal villus height and villus surface area in the piglet jejunum. Collectively, this work establishes a porcine model of intestinal injury for designing novel nutritional means to improve gut function in pigs and humans.