Bilateral superior vena cava (SVC), which occurs following bilateral bidirectional cavopulmonary shunt (BCPS), is an anomaly marked by unique hemodynamics. This study aimed to determine its effects on outcomes after Fontan completion. Among 405 patients who underwent BCPS and total cavopulmonary connection (TCPC) between 1997 and 2017, 40 required a bilateral-BCPS. The dominant SVC prior to TCPC was identified according to the direction of blood flow in the central pulmonary artery, and its relationship to the inferior vena cava (IVC) was classified as a concordant or discordant relationship. Preoperative factors were analyzed to identify the risk factors for specific adverse outcomes. The length of intensive care unit (ICU) stay after TCPC was longer in the 40 patients who underwent bilateral-BCPS than in those who underwent unilateral BCPS (p = 0.024), and the survival rate was lower in the former group than in the latter group (p = 0.004). In the patients who underwent bilateral-BCPS, the dominant SVC was concordant with the IVC in 30 patients and discordant in 10 patients. With regard to whether certain morphological, hemodynamic, and flow dynamics-related variables were risk factors for adverse outcomes following TCPC, a discordant relationship between dominant SVC and IVC was identified as an independent risk factor for both a longer ICU stay (p = 0.037, HR 2.370) and worse survival (p = 0.019, HR 13.880). Therefore, in patients with a bilateral SVC who have previously undergone bilateral-BCPS, a discordant relationship between dominant SVC and IVC might contribute to worse outcomes following TCPC.