We previously showed a prophylactic effect of Lactobacillus pentosus strain S-PT84 against oral candidiasis in mice. In the present study, we evaluated the protective effect of S-PT84 against Candida infection of the gastrointestinal tract. As the first step, we used an in vitro assay to compare the inhibitory effects of several lactobacilli (S-PT84 and Lactobacillus pentosus type strain JCM1558T, Lactobacillus gasseri type strain JCM1131T and Lactobacillus casei type strain JCM1134T) on mycelial growth of Candida albicans. S-PT84 directly adhered to Candida cells and showed the strongest growth-inhibitory activity among the tested Lactobacillus strains. In the second experiment, we used an in vivo assay to evaluate the effect of S-PT84 ingestion on severity score of stomach lesion and gastric inflammation in a mouse model of gastrointestinal candidiasis. The severity scores were significantly improved by oral administration of S-PT84 (6 mg/ 200 μL), consistent with decreased coverage of stomach lesions by patchy whitish plaques. The attenuation of stomach lesion severity by S-PT84 was more pronounced than that obtained with L. gasseri type strain JCM1131T, consistent with the results of the above in vitro study. Histological analysis also indicated that S-PT84 prevented the adhesion of C. albicans to the stomach surface and suppressed stomach inflammation caused by neutrophil infiltration. Furthermore, S-PT84 also suppressed the vascular permeability observed in Candida-infected stomach. These results suggest that oral administration of S-PT84 might be effective not only in inhibiting Candida infection but also in preventing gastric inflammation induced by Candida infection.