The dysbiosis of gut microbiota may cause many complications in patients with end-stage renal disease, which may be alleviated by probiotic, prebiotic, and synbiotic supplementation. The aim of this systematic review and meta-analysis was to assess the effects of these supplementations on circulatory uremic toxins, biomarkers of inflammation, and oxidative stress in hemodialysis patients. We searched the EMBASE, MEDLINE, Web of Science, and Cochrane Library databases until 8 August 2021. Randomized controlled trials evaluating adult patients receiving hemodialysis were included. The pooled results from 23 studies with 931 hemodialysis patients indicated that interventions significantly decreased the circulating levels of p-cresyl sulfate (standardized mean difference (SMD): 0.38; 95% CI: −0.61, −0.15; p = 0.001), endotoxins (SMD: −0.58; 95% CI: −0.99, −0.18; p = 0.005), malondialdehyde (SMD: −1.16; 95% CI: −1.81, −0.52; p = 0.0004), C-reactive proteins (CRP) (SMD: −0.61; 95% CI: −0.99, −0.23; p = 0.002), and interleukin 6 (SMD: −0.92; 95% CI: −1.51, −0.33; p = 0.002), and improved the total antioxidant capacity (SMD: 0.89; 95% CI: 0.49, 1.30; p < 0.0001) and glutathione (SMD: 0.40; 95% CI: 0.14, 0.66; p = 0.003) when compared to the placebo group. Our results suggest that treatment with probiotics, prebiotics, and synbiotics may help alleviate uremic toxin levels, oxidative stress, and the inflammatory status in hemodialysis patients.