Objective: To summarize and assess the effects of probiotic preparations on inflammatory cytokine levels in patients with Chronic Kidney Disease (CKD). Methods: We searched through the PubMed, Cochrane Library, Embase, Web of Science, China National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature Database (CBM), and Wan Fang databases for Randomized Controlled Trials (RCTs) that report the impact of probiotic preparations on inflammatory cytokines in CKD patients. Outcomes were composed of serum levels of CReactive Protein (CRP), Interleukin 6 (IL-6), Tumor Necrosis Factor-α (TNF-α), serum urea, creatinine, uric acid, Para-Cresol Sulfate (PCS), and Indoxyl-Sulfate (IS). The Mean Differences (MDs) with 95% Confidence Intervals (CIs) were considered as effect estimates. Sensitivity analysis and Egger’s linear regression test were performed to evaluate the stability of results and publication bias. This study was registered with PROSPERO number CRD42020176557. Results & Discussion: Sixteen studies met the inclusion criteria. Evidence showed that serum CRP levels were decreased in the intervention group (WMD, -12.29, 95% CI, -16.41 to -8.16, p = 0). The IL-6 was significantly reduced only in the prebiotic group (SMD, -0.73, 95% CI, -1.3 to -0.16, p = 0.012). However, no reduction was observed in TNF-α (SMD, -0.07, 95% CI, -0.51 to 0.38, p = 0.772). Moreover, there was no significant change in serum uremic toxin, including creatine, urea, uric acid, PCS, and IS. Conclusions: Probiotic preparations decrease the serum levels of inflammatory cytokines in CKD patients but do not affect the serum uremic toxin levels. The results of this meta-analysis suggest essential guidance for treatment decisions in clinical practice.