An intractable pleural effusion is a common comorbidity of a Fontan operation, occasionally leading to undesirable outcomes. The preventive effect of aortopulmonary collateral (APC) coil embolization against a pleural effusion before a Fontan operation is still controversial. This is a retrospective single-center study; among 227 Fontan cases, 57 cases with complete MRI data were analyzed at first. Factors associated with the duration of pleural drainage (median: 6 (2-41) days) and that of postoperative hospital stay (median: 25 (14-91) days) were analyzed using a multiple regression analysis. The pulmonary artery index (PAI; Nakata index) was associated with both the pleural drainage duration (P < 0.05, r 2 = 0.17) and postoperative hospital stay (P < 0.05, r 2 = 0.10).Thereafter, all the 227 patients were classified into the following three groups: Group A (12 patients in whom the embolization was performed within 30 days before the Fontan surgery), Group B (131 patients in whom the embolization was performed more than 30 days before the Fontan surgery), and Group C (84 patients in whom the embolization was not performed). Patients in Group A were found to be associated with the shortest length of both periods (P < 0.05).Lower PAI values were related to a prolonged pleural drainage duration and postoperative hospital stay. APC coil embolizations may reduce the risk if they are performed shortly (less than 30 days) before the operation.