Although early postoperative outcomes after Fontan improved in the modern era, the convincing evidence in the resource-scare setting was sparse. Our study aimed to determine the incidence of early Fontan failure (EFF) in a contemporary series of palliated patients and to identify its potential risk factors. A single-center retrospective study was conducted between 2012 and 2019 on 145 patients undergoing the Fontan procedure. The primary outcome of interest was EFF, defined as death, Fontan takedown, or listing for heart transplantation prior to hospital discharge or within 30 postoperative days. Our study reported the incidence of EFF of 9.66% (n = 14: thirteen deaths, and one Fontan takedown). In the univariate analysis for pre-operative data, the anatomical diagnosis of unbalanced atrioventricular (AV) septal defect, situs inversus form, AV valve regurgitation, large aorta-pulmonary circulation in Doppler echocardiography, elevated pulmonary artery pressure (PAP), and elevated pulmonary vascular resistance were significantly associated with EFF. At the Fontan, four risk factors influencing EFF included pulmonary artery reconstruction, AV valve repair, bleeding, and elevated PAP. Post-operative edema was also significantly associated with EFF. A final reduced model with multivariate logistic regression analysis indicated preoperative elevated PAP, AV valve repair at Fontan, and postoperative elevated PAP were independent predictors for EFF. In conclusion, EFF is relatively high in our series, and is associated with significant mortality. Patients with a single ventricle physiology undergoing preoperative elevated PAP, AV valve repair at Fontan, and postoperative elevated PAP were identified as independent risk factors to predict EFF.