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Probiotics and peptides might can improve exercise performance. However, the effects of the combination of the two on athletic performance remains unclear. This study analyzed the effects of administering yeast polypeptide (YP) and/or Lacticaseibacillus casei Zhang (LCZ) on exercise performance in rats. The rats were randomized into four groups for 10-week dietary intervention, namely normal control (NC), polypeptide (YP), probiotics (LCZ, 4 × 109 CFU/d), and YP plus LCZ (YPZ). Then, a forced running-wheel protocol was implemented for three weeks. The multiple parameters, including exercise time, immune factors, gut microbiota, and serum metabolites were monitored. This study demonstrated that co-administering YP and LCZ significantly improved rats’ exercise time, and the beneficial effects were likely achieved through influencing the gut microbiota and serum metabolites. Our study presented a new method to improve exercise performance by supplementing with probiotics and yeast peptides, which may provide a new strategy for the development of functional foods.