Abstract Background Some inborn errors of metabolism (IEMs) resulting in aberrations to blood leucine and ammonia levels are commonly treated with kidney replacement therapy (KRT). Children with IEMs require prompt treatment, as delayed treatment results in increased neurological and developmental morbidity. Objectives Our systematic review in neonates and pediatrics evaluates survival rates and reductions in ammonia and leucine levels across different KRT modalities (continuous KRT (CKRT), hemodialysis (HD), peritoneal dialysis (PD)). Data sources A literature search was conducted through PubMed, Web of Science, and Embase databases for articles including survival rate and toxic metabolite clearance data in pediatric patients with IEM undergoing KRT. Study eligibility criteria Cross-sectional, prospective, and retrospective studies with survival rates reported in patients with IEM with an intervention of CKRT, PD, or HD were included. Studies with patients receiving unclear or multiple KRT modalities were excluded. Study appraisal and synthesis methods Analysis variables included efficacy outcomes [% reduction in ammonia (RIA) from pre- to post-dialysis and time to 50% RIA] and mortality. The Newcastle Ottawa Risk of Bias quality assessment was used to assess bias. All statistical analyses were performed with MedCalc Statistical Software version 19.2.6. Results A total of 37 studies (n = 642) were included. The pooled proportion (95% CI) of mortality on CKRT was 24.84% (20.93–29.08), PD was 34.42% (26.24–43.33), and HD 34.14% (24.19–45.23). A lower trend of pooled (95% CI) time to 50% RIA was observed with CKRT [6.5 (5.1–7.8)] vs. PD [14.4 (13.3–15.5)]. A higher mortality was observed with greater plasma ammonia level before CKRT (31.94% for ≥ 1000 µmol/L vs. 15.04% for < 1000 µmol/L). Conclusions and implications of key findings Despite the limitations in sample size, trends emerged suggesting that CKRT may be associated with lower mortality rates compared to HD or PD, with potential benefits including prevention of rebound hyperammonemia and improved hemodynamic control. While HD showed a trend towards faster achievement of 50% RIA, all modalities demonstrated comparable efficacy in reducing ammonia and leucine levels. Prospero registration CRD42023418842. Graphical abstract