Introduction: Peritoneal dialysis and continuous renal replacement therapy (CRRT) are the most frequently used treatment modalities for acute kidney injury. CRRT is currently being used for the treatment of several non-renal indications, such as congenital metabolic diseases. CRRT can efficiently remove toxic metabolites and reverse the neurological symptoms quickly. However, there is not enough data for CRRT in children with metabolic diseases. Therefore, we aimed a retrospective study to describe the use of CRRT in metabolic diseases and its associated efficacy, complications, and outcomes. Materials and Methods: We performed a retrospective analysis of the records of all patients admitted in the pediatric intensive care unit (PICU) for CRRT treatment. Results: Between December 2014 and November 2018, 97 patients were eligible for the present study. The age distribution was between 2 days and 17 years, with a mean of 3.77 +/- 4.71 years. There were 13 (36.1%) newborn with metabolic diseases. The patients were divided into two groups: CRRT for metabolic diseases and others. There was a significant relationship between the groups, including age (p 0.001), weight (p = 0.028), blood flow rate (p 0.001); dialysate rate (p 0.001), and replacement rate (p 0.001). The leucine reduction rate was 3.88 +/- 3.65 (% per hour). The ammonia reduction rate was 4.94 +/- 5.05 in the urea cycle disorder group and 5.02 +/- 4.54 in the organic acidemia group. The overall survival rate was 88.9% in metabolic diseases with CRRT. Conclusion: In particularly hemodynamically unstable patients, CRRT can effectively and quickly reduce plasma ammonia and leucine.