Genetic epilepsies, such as KCNQ2 gene variants, though uncommon, are potential causes of neonatal seizures in infants with complex congenital heart disease (CHD). KCNQ2-related seizures commonly present as tonic posturing with autonomic changes and a distinctive amplitude-integrated EEG (aEEG) pattern with increase in amplitude immediately followed by background suppression. Seizures are typically refractory to commonly used antiepileptics in this age group and respond best to sodium channel blockers such as carbamazepine and fosphenytoin. We report the cases of two neonates with complex CHD who presented with seizures secondary to KCNQ2 gene variation and how early recognition of clinical and EEG features led to early treatment and improved seizure burden. When investigating the etiology of neonatal seizures in the perioperative complex cardiac infant, genetic etiologies, such as KCNQ2 variants should be considered, particularly in the absence of clinical exam and neuroimaging features consistent with brain injury. These two cases highlight the importance of a precision medicine approach utilizing clinical examination and seizure semiology, bedside aEEG monitoring, genetic testing, and targeted treatments to improve patient care and outcomes.