OBJECTIVE As the surgical results for Fontan candidates improve, much attention has been given to the long-term cognitive outcomes. This study aimed to assess the neurocognitive outcomes after Fontan completion, and to determine the factors associated with an extremely low intelligence quotient (IQ <70). METHODS A total of 70 local eligible school-aged patients were enrolled in the study (hypoplastic left heart syndrome, 17; right atrial isomerism, 15 and others, 38). Fontan operations were performed at a median age of 1.8 (range, 0.5-8.9) years (primary Fontan, 4 of 70 [6%]). The Wechsler Intelligence Test was taken at a median age of 9 (range, 5.1-14.4) years for the purpose of neurocognitive evaluation. Patients' data were collected from medical records, and a retrospective analysis of potential predictors for an IQ <70 was performed. RESULTS The median full-scale IQ (FSIQ) for the entire cohort was 85 (range, 43-118). Of the lower order composites, the perceptual reasoning index and the working memory index were significantly lower in low-FSIQ patients (P < 0.05). Overall, 15 of 70 (21%) of the cohort had an IQ <70. Univariate analysis identified three significant risk factors for FSIQ <70 (15 of 70, 21%): body weight <2.5 kg at initial palliative surgery (P < 0.05), low 5-min Apgar score <4 (P < 0.05) and inter-stage events requiring cardiopulmonary resuscitation (CPR) (P < 0.05). No other patient-specific factors (e.g. cardiac morphology) or modifiable surgical factors (e.g. the use of hypothermic cardiac arrest) were associated with FSIQ <70. CONCLUSIONS Low body weight (<2.5 kg) at initial operation, low 5-min Apgar score (<4) and inter-stage CPR were significant risk factors for impaired neurocognitive outcomes. An evolving strategy for preventing inter-stage CPR may improve cognitive outcomes.