© 2019 The Authors The heat-inactivated, enteric-colonizing Lactobacillus gasseri CP2305 (CP2305) ameliorates psychological stress-related symptoms. In this study, we examined effects of CP2305 on top athletes experiencing physical and mental stresses. Forty-nine male university Ekiden (long distance relay race) runners daily took the CP2305-containing beverage for 12 weeks during training for and competing in All-Japan university championships. The CP2305 intake significantly facilitated recovery from fatigue and relieved anxiety and depressive mood, compared with placebo intake. The CP2305 intake significantly prevented the training-induced reduction of hemoglobin and facilitated exercise-induced increase in serum growth hormone levels. The CP2305 intake significantly increased the alpha- and beta-diversities of fecal microbiota, and the compositions of Bifidobacterium and Faecalibacterium. Gene expression profiling of peripheral blood leukocytes indicated that CP2305 prevented the stress-induced changes in the expression of genes related to mitochondrial functions. Our results suggest that daily intake of paraprobiotic CP2305 may be beneficial to athletes facing stressful situations.