Background Achieving optimal hepatic factor distribution and total cavopulmonary resistance is crucial for long-term outcomes in single ventricle palliation patients. Y-shaped Gore-Tex Fontan procedure redirects hepatic drainage to both the right and left pulmonary arteries. The aim of this approach is to achieve bilateral pulmonary distribution of hepatic factors and reduce the risk of arteriovenous malformations that can develop in single-ventricle patients. Case presentation We present a unique case of a 20 years old female with symptoms of heart failure, who has a history of complex heterotaxy with polysplenia, interrupted Inferior vena-cava, and double outlet right ventricle with unbalanced atrio-ventricular septal defect, d-malposed great arteries, and pulmonary atresia. Fenestrated Y-shaped Gore-Tex Fontan procedure was successfully done which was confirmed by performing cardiac CT angiography. Conclusions Studies have shown that achieving balanced hepatic factor distribution and low resistance in the Fontan pathway can improve long-term outcomes. This procedure has demonstrated positive results in terms of oxygen saturation and reduced asymmetric blood flow distribution. Level of Evidence Level 4, Case Report.