Purpose ABO-incompatible (ABO-i) liver transplantation (LT) is a life-saving method for pediatric patients in emergency situations that has the potential to expand the pool of liver donors. However, the risks of ABO-i compared to ABO-compatible (ABO-c) LT are unclear. To address this clinical uncertainty, we conducted a systematic review and meta-analysis to compare clinical outcomes between ABO-i and ABO-c LT in pediatric patients. Methods A systematic search for studies comparing outcomes between ABO-i and ABO-c LT was performed in the MEDLINE (PubMed), EMBASE, and Cochrane Library databases through May 2020. Outcomes evaluated included graft survival rate, patient survival rate, rejection, infection, biliary complications, and vascular complications. Quality of evidence was assessed using the Newcastle-Ottawa scale. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using RevMan 5.3. Results A total of 12 studies involving 7461 patients were included in the review. Meta-analysis of these studies showed significantly lower 1 year, 3 year, and 5 year graft survival rates for ABO-i vs. ABO-c LT (1 year: OR = 0.46, 95% CI 0.35-0.59,P < 0.00001; 3 years: OR = 0.47, 95% CI 0.36-0.63,P < 0.00001; 5 year: OR = 0.48, 95% CI 0.37-0.63,P < 0.00001) as well as significantly lower 1 year, 3 year, 5 year, and 10 year patient survival rates for ABO-i vs. ABO-c (1 year: OR = 0.34, 95% CI 0.24-0.49,P < 0.00001; 3 years: OR = 0.24, 95% CI 0.14-0.40, P < 0.00001; 5 years: OR = 0.47, 95% CI 0.35-0.64,P < 0.00001; 10 years: OR = 0.59, 95% CI 0.38-0.90,P = 0.02). No significant differences were observed between the groups in incidence of cytomegalovirus infection, acute cellular rejection, acute rejection, biliary complications, or hepatic artery thrombosis. Conclusions Our systematic review and meta-analysis showed consistently lower patient survival and graft survival in pediatric ABO-i LT compared to ABO-c LT. However, ABO-i LT is still a life-saving emergency option for pediatric patients waiting for a suitable liver source.