Background Direct oral anticoagulants (DOACs) have been widely applied in adults for thrombosis prophylaxis. However, the effect of DOACs in pediatric patients with congenital or acquired heart diseases who need anticoagulation therapy remains unclear.Methods We systematically searched the databases of PubMed, Embase, and the Cochrane Library, as well as the ClinicalTrials.gov registry and the World Health Organization's International Clinical Trials Registry Platform until June 2024 to identify relevant randomized clinical trials (RCTs). If the number of included studies was less than 5, we performed a narrative review to assess the effect of DOACs in pediatric patients.Results Four studies were included. In the UNIVERSE study, thrombotic events occurred in 2% of the rivaroxaban group and 9% of the aspirin group, with bleeding events in 36% and 41%, respectively. The ENNOBLE-ATE study showed no thromboembolic events in the edoxaban group and 1.7% in the SOC group (rate difference: -0.07%, 95% CI: -0.22 to 0.07%). Major bleeding rates were similar (rate difference: -0.03%, 95% CI: -0.18 to 0.12%). The SAXOPHONE trial showed no thromboembolic events in either group and similar major bleeding rates (-0.8%, 95% CI: -8.1 to 3.3%). In the DIVERSITY trial, 81% of dabigatran patients achieved the primary outcome versus 59.3% in the SOC group (Odds ratio: 0.342, 95% CI: 0.081-1.229). No major bleeding occurred in either group.Conclusion Existing studies suggest that the use of DOACs hold promise as an effective and safe alternative for preventing and treating thromboembolism in pediatric patients with heart conditions.