Background: Probiotic supplementation in infancy is increasingly used to support immune development, particularly through modulation of mucosal immunoglobulin A (IgA) and systemic cytokines. However, the overall immunological impact of probiotics in infants remains uncertain. Methods: We conducted a systematic review and meta-analysis of randomised controlled trials (RCTs) from 2000 to 2025, assessing the effects of oral probiotic supplementation on faecal IgA and cytokine levels in infants. Random-effects models were used to estimate pooled effects. IgA outcomes were analysed using weighted mean differences (WMD), and cytokine outcomes (reported as medians) were pooled using the quantile estimation (QE) method. Results: Forty-two RCTs were included: 24 reporting IgA and 18 reporting cytokine outcomes. Seven IgA and eight cytokine studies were eligible for meta-analysis. The pooled effect of probiotics on faecal IgA was not statistically significant (WMD = 87.54 µg/g; 95% CI: −408.05 to 583.12; I 2 = 89%). However, after removing one outlier, the effect became significant (WMD = 421.36; 95% CI: 161.31-681.41; I 2 = 0%). Cytokine meta-analyses (IL-10, IL-6, TNF-α, IFN-γ) showed no consistent effects, though individual studies indicated increases in IL-10 and reductions in TNF-α and IL-17A. Narrative synthesis highlighted heterogeneity by strain, feeding mode, and measurement timing. Conclusion: Probiotics may modestly enhance mucosal immunity in infancy, as shown by increased faecal IgA in sensitivity analysis. Systemic cytokine responses remain inconsistent. These findings support the immunomodulatory potential of probiotics in early life and underscore the need for standardised outcomes and extended follow-up in future trials.