Probiotics are now prevalent world-wide, as functional food supplements with many benefits for humans and animals, such as protective effects against pathogenic infection. We showed that oral supplementation of Lactobacillus pentosus AT6 (AT6) decreased the mortality rate of mice with Salmonella infection. A series of experiments showed that the protective effects of AT6 on mice involved multiple mechanisms, including (1) the inhibition of Salmonella Typhimurium growth by AT6 or its cell-free culture supernatants (CFCSs); (2) the reduction of the bacterial loads of Salmonella Typhimurium in intestinal contents and internal organs, such as the liver and spleen; (3) the inhibition of adhesion and invasion of Salmonella Typhimurium into intestinal epithelial cells; and (4) the regulation of host immunities by modifying the production of a chain of cytokines. In conclusion, AT6 inhibited Salmonella infection via multiple mechanisms and therefore has great potential for the development of functional foods with anti-Salmonella activities.