Fontan operation in heterotaxy patients has been associated with high mortality. We studied whether adoption of the extracardiac conduit (EC) total cavopulmonary connection (TCPC)in heterotaxy demonstrated comparable results to non-heterotaxy population. A retrospective medical record review of 35 consecutive patients with heterotaxy and 70 consecutive patients without heterotaxy syndrome who underwent EC TCPC between 2000 and 2018 was performed. In the 35 heterotaxy patients, 30 were right and 5 were left atrial isomerism. Anomalies of venous return included bilateral superior vena cava in 20 (57.1%), separated hepatic vein in 8 (22.9%), interrupted inferior vena cava in 3 (8.6%), total anomalous pulmonary venous return in 7 (20%), and partial in 2 patients (5.7%). All patients underwent EC TCPC under beating-heart cardiopulmonary bypass except in four patients (11.4%) cardioplegic arrest was needed for cardiac repair. The surgical mortality rate was lower in heterotaxy patients (0% vs. 5.7%; p = 0.299) but statistically not significant. The follow-up ranged from 2 months to 17.8 years (mean 9.4 ± 5.6 years). At 15 years, there was no significant difference between the heterotaxy and non-heterotaxy patients regarding the long-term survival (70% vs. 78.6%; p = 0.443), freedom from reoperation (81.9% vs. 96.5%; p = 0.057), and postoperative arrhythmia (17.1% vs. 7.1%; p = 0.174). EC TCPC can be performed in heterotaxy patients with comparable early and late results to the non-heterotaxy population. However, the late morbidities regarding the Fontan circulation needs careful follow-up.