Computational fluid dynamics (CFD) is a tool that allows for the analysis of otherwise unobservable blood flow patterns. In the context of medicine, CFD enables researchers to better understand acute and chronic pathophysiology as well as utilize modeling tools to predict blood flow patterns in response to surgical intervention. Such a tool is particularly useful in the field of congenital heart disease (CHD), where complex geometries and patient-specific pathology are common. Research applying CFD to study CHDs has significantly grown in the last twenty years, with new methodologies and recommendations being published at an even faster pace in the last decade. Many currently available reviews are focused on a particular area of progress or on the technical approaches to CFD geared toward the clinician. This review focuses on CFD application within the major domains of CHD research, specifically single ventricle defects and aortic coarctation, reviewing consensus seminal work while highlighting more recent avenues of study. Balancing discussion of CFD parameters with potential clinical implications of study results, this review not only aims to provide cardiovascular professionals context for the technical advancements being made in the field but also a sense of contemporary CFD’s utility in clinical practice.