With improvements in treatment of congenital heart disease more paediatric patients are surviving with palliative or corrective interventions during childhood, thus becoming adults with congenital heart disease (ACHD). Overall, the ACHD population is at a higher risk of arrhythmias and stroke. The abnormal structure and function of their corrected hearts suggests that in addition to established stroke risk factors, such as prior stroke or older age, additional stroke risk factors need to be considered to determine the risk and establish the indication for oral anticoagulation (OAC) in ACHD patients. In structurally normal hearts non-vitamin-K oral anticoagulants (NOACs) offer at least equal stroke prevention with a better safety profile compared to vitamin K antagonists (VKA) in patients with atrial fibrillation (AF) or pulmonary embolism. Current guidelines recommend NOACs in ACHD patients with simple lesions and indication for OAC, while there is less certainty about their safety in ACHD patients with moderate or complex congenital heart disease such as patients with transposition of the great arteries (TGA) after atrial switch operation (Senning or Mustard operation), Fontan circulation or congenital corrected transposition of the great arteries (ccTGA). This review summarises the available evidence characterising stroke risk in patients with ACHD and the use of anticoagulants and interventional therapies to reduce that risk.