Complex cardiac anomalies are sometimes channeled toward Fontan palliation for various reasons. Nevertheless, anatomical repair after bidirectional cavopulmonary shunt may be another option with theoretical benefits. In this study, we report our experience with anatomical repair conversion in challenging patients who had been palliated with bidirectional cavopulmonary shunt. Retrospective review was conducted in patients who underwent anatomical repair conversion from prior bidirectional cavopulmonary shunt palliation between January 2008 and March 2016. Patients who underwent a planned staged 1½-ventricular repair were excluded. Twenty-three patients underwent anatomical repair conversion at a median age of 6.5 years (range 2.7–20.0 years). The interval time between palliation and conversion was 4.6 ± 2.4 years (range 0.9–12.4). Indications for conversion were high-risk Fontan candidates (n = 11) and preference for biventricular anatomy (n = 12). In eight of the patients, bidirectional cavopulmonary shunts were taken down and superior vena cava was reconnected to the right atrium with Gore-Tex tube or bovine jugular venous tube. Mean cardiopulmonary bypass and aortic cross-clamp times were 225.6 ± 107.0 and 138.3 ± 76.6 min, respectively. After a mean follow-up of 2.7 ± 2.2 years, there was no mortality and reoperation. No patients presented sinoatrial node dysfunction and superior venous cave stenosis. All the patients were in the New York Heart Association functional class I or II. Patients with previous bidirectional cavopulmonary shunt should be re-evaluated before completion of Fontan and, if cardiac anatomy allows, anatomical repair conversion may be considered, especially in patients with high-risk Fontan completion. Initial bidirectional cavopulmonary shunt palliation should not be considered as a one-way path to Fontan. Although technically challenging, early- and mid-term clinical results of anatomical repair conversion were satisfactory.