An enteral formula containing fermented milk products and prebiotics (prebiotic formula, PF) is known to promote the proliferation of Bifidobacterium and the production of short-chain fatty acids (SCFAs) in humans and rats. We studied the effect of PF on the secretion of glucagon-like peptide-1 (GLP-1) and the involvement of SCFAs in this process, using the knockout (KO) mice for the SCFA receptors G protein-coupled receptor 41 (GPR41) and G protein-coupled receptor 43 (GPR43). Wild type (WT) or KO mice were fed either a standard formula (SF) or PF for two weeks, and then were orally administered either PF or SF after overnight fasting and dissected after 0, 30, 60, and 240 minutes. Blood GLP-1 and glucose levels were measured (Experiment 1). Alternatively, mice fed SF or PF for two weeks were dissected after four hours of fasting, and their blood GLP-1 and cecal SCFAs levels were measured (Experiment 2). In Experiment 1, WT and GPR43KO mice showed a significant increase in GLP-1 concentration 30 and/or 60 minutes after formula administration in the PF group compared with that in the SF group. Similarly, WT and GPR43KO mice showed a significant suppression of the increase in glucose levels after formula administration in the PF group compared with that in the SF group. On the other hand, there was no significant difference in GLP-1 concentration or blood glucose levels between the two treatment groups in GPR41KO mice. In Experiment 2, there was a significant increase in cecal SCFA levels in the PF group compared with that in the SF group for all mice, as well as an increase in GLP-1 concentration. PF promotes GLP-1 secretion and SCFAs might contribute to the GLP-1 secretion that occurs directly after ingestion, through GPR41 signal transduction.