The benefits of prophylactic anticoagulation or antiplatelet therapy for patients undergoing extracardiac conduit (ECC) Fontan procedure still are a matter of debate. Through a systematic review and meta-analysis, this study aimed to determine the incidence of thromboembolism among patients undergoing ECC Fontan who received anticoagulation or antiplatelet therapy. Until February 2010, MEDLINE studies describing the incidence of thromboembolic events after ECC Fontan were reviewed. Information on type of drugs and clinical outcome was extracted. The 20 studies analyzed involved 1,075 patients: 220 (20.4%) in the antiplatelet group and 855 (79.5%) in the anticoagulation group. The mean follow-up period ranged from 2 to 144 months. The overall thromboembolism rate was 5.2% (95% confidence interval [CI], 3.8–7%; I² = 0%; p_het = 0.32). The effect of different therapeutic strategies on the occurrence of thromboembolic and bleeding events was analyzed. Interestingly, the anticoagulation therapy compared with the antiplatelet therapy was not associated with a significant reduction in the incidence of overall thromboembolic complications (5% vs 4.5%, respectively; I² = 0%; p_het = 0.80). Only two cases of bleeding were observed among patients receiving anticoagulant therapy at the time of the event. For patients undergoing ECC Fontan, the rate of thromboembolic and bleeding events associated with antiplatelet therapy is similar to that associated with anticoagulation therapy.