Background and Objectives: Probiotic supplementation can prevent and alleviate gastrointestinal and respiratory tract infections in healthy individuals. Markers released from the site of inflammation are involved in the response to infection or tissue injury. Therefore, we measured the pre-exercise and postexercise levels of inflammation-related markers-tumor necrosis factor (TNF)-α, interleukin (IL)-6, IL-8, IL-10, interferon (IFN)-γ, salivary immunoglobulin A (IgA), IL-1β, IL-2, IL-4, and C-reactive protein (CRP)-in probiotic versus placebo groups to investigate the effects of probiotics on these markers in athletes. Probiotics contained multiple species (e.g., Bacillus subtilis, Bifidobacterium bifidum, etc.). Materials and Methods: We performed a systematic search for studies published until May 2022 and included nine randomized clinical trials. Reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses guideline. Fixed-effects meta-analyses and sensitivity analyses were performed. Subgroup analyses were conducted on the basis of the period of probiotic intervention and timing of postassessment blood sampling. Results: The levels of IFN-γ and salivary IgA exhibited a significant positive change, whereas those of TNF-α and IL-10 demonstrated a negative change in the probiotic group. The subgroup analysis revealed that the probiotic group exhibited significant negative changes in TNF-α and IL-10 levels in the shorter intervention period. For the subgroup based on the timing of postassessment blood sampling, the subgroup whose blood sample collection was delayed to at least the next day of exercise exhibited significant negative changes in their TNF-α and IL-10 levels. The subgroups whose blood samples were collected immediately after exercise demonstrated negative changes in their TNF-α, IL-8, and IL-10 levels. Conclusions: Probiotic supplementation resulted in significant positive changes in the IFN-γ and salivary IgA levels and negative changes in the IL-10 and TNF-α levels. No significant changes in the IL-1β, IL-2, IL-4, IL-6, IL-8, or CRP levels were observed after probiotic use in athletes.