Tetralogy of Fallot (ToF) is the most prevalent cyanotic congenital heart disease. Genetic syndromes are present in up to one quarter of patients with this condition, leading to increased morbidity and mortality. Our aim in this work is to characterize our population, evaluate ToF based on the presence of genotype anomalies, and investigate early intervention predictors and outcomes. A retrospective study was performed on neonates with ToF born between August 1, 2008, and August 31, 2018, and admitted to a level III neonatal intensive care unit (NICU). Patients were categorized based on the presence of genotype anomalies and timing of intervention. Thirty-nine neonates were included. The overall mortality during the follow-up period was 5.1% (n = 2). Threatened preterm labor/preterm labor was more prevalent in patients with associated genotype anomalies (p = 0.015). Multivariate analysis showed an association between an abnormal amount of amniotic fluid and ToF with altered genotype, adjusted for smoking, maternal age, gestational age and birth weight [OR = 29.92, 95% CI (1.35–662.44), p = 0.032]. We also found an association between cesarean delivery and neonatal procedures (p = 0.006). Mortality was significantly higher in neonates who underwent early intervention (p = 0.038). Our results indicate that an abnormal amount of amniotic fluid is an independent predictive factor for ToF with genotype alterations. This finding could ultimately have an impact on both prenatal and neonatal counseling and management.