Congenital heart disease is among the most common birth defects encountered. Stroke may occur as a consequence of the underlying heart defect itself, or secondary to life-saving cardiothoracic surgical procedures. Advancements in surgical techniques and improved survival require a new assessment of the epidemiology, risk factors, prevention and treatment options of stroke in the pediatric population. In this review, we discuss the most common associations between cardiothoracic interventions and stroke and review evaluation and treatment options.