Central vascular thrombosis (CVT) in critically ill neonates carries significant clinical implications. Neonates with congenital heart disease (CHD) awaiting cardiac intervention might be associated with increased risk of thrombosis. Outcome analysis was undertaken. An analysis of 77 neonates with CHD who were admitted to the NICU prior to cardiac intervention between January 2015 and December 2016 was undertaken. Patients requiring extracorporeal life support prior to any cardiac intervention, or receiving prophylactic anticoagulation not related to central vascular catheter (CVC) were excluded. Diagnosis of CVT was provided based on clinical indication and verified with imaging that warranted anticoagulation therapy. Location of CVC and extent of CVT along with treatments, outcomes, and vascular access types and durations were assessed. Logistic regression multivariate analysis was used to assess predictors of outcome. Neonates with CHD were complicated with CVT in 10.4%. Longer duration of CVC was also associated with thrombosis in neonates with CHD (72.7 days vs. 29.3 days, p < 0.001). Independent predictors of outcome included lower gestational age and CHD with single-ventricle (SV) anatomy (p < 0.05). In neonates with CHD awaiting cardiac intervention risk of CVT is substantial. Duration CVC, lower gestational age and SV anatomy are risk determinants of outcome. Standardized development of customized surveillance protocols tailored to this unique subsets of neonates and adherence to quality guidelines can influence outcome.