The intestine is the largest immune and metabolic site in the body and is thus important for animal health. The integrity of the mucosal barrier and function are fundamental factors protecting the health of the intestine. Stress has been reported to have profound effects on the gastrointestinal tract, including altering gut permeability, the intestinal barrier, and homeostasis. Tryptophan is a functional essential amino acid that alters the gut microbiota and regulates intestine structural and functional change, thus contributing to host physiology and metabolism. Changes in tryptophan metabolism and its metabolites in brain and intestinal tissues during stress suggest that tryptophan may play an important role in the stress response. We therefore review the literature on the mechanisms underlying stress-related diseases and the role of tryptophan metabolism in the regulation of gut homeostasis, with particular focus on functional bowel disorders and their relationship to stress, to provide a theoretical foundation for targeting tryptophan in stress-related intestine diseases.