Currently, the extracardiac conduit total cavopulmonary connection (eTCPC) is the most widely used for Fontan modification worldwide. Nevertheless, there have been some cases that are difficult for performing eTCPC because of their anatomical complexity, such as apicocaval juxtaposition. For such cases, in 2002, we introduced the intra-extracardiac TCPC (ieTCPC). We reviewed our 20-year single-center experience with 316 TCPC patients to compare eTCPC (n = 277) and ieTCPC (n = 39) in terms of mortality and morbidity. ieTCPC was indicated for the cases in which there was concern that the TCPC conduit would be too curved for ordinary eTCPC. Early death occurred in 1 patient and late death occurred in 15 patients. The actuarial survival rate in the eTCPC and the ieTCPC groups at 10 years were 95.1% and 100.0%, respectively. There was no significant difference in actuarial survival between eTCPC and ieTCPC patients. In the multivariate analysis, preoperative superior vena cava pressure and preoperative oxygen saturation were found to be the independent predictor for postoperative mortality. There was also no significant difference in actuarial rate of freedom from late-occurring complications between eTCPC and ieTCPC groups. In the multivariate analysis, dominant right ventricle and preoperative SVC pressure were independent predictors for late-occurring complications. The clinical outcomes in patients who undergo eTCPC and ieTCPC appear to be excellent, with low mortality and morbidity rates in the midterm. ieTCPC may be a good option for TCPC cases with anatomical complexity such as apicocaval juxtaposition and separated hepatic vein drainage.