Advances in medical care have significantly extended the lifespan of patients with congenital heart disease (CHD), allowing most to survive into adulthood. However, they continue to face significant cardiovascular morbidity, particularly atrial arrhythmias (AA), heart failure, and thromboembolic (TE) events. TE events in adult CHD patients arise from various factors, including AA, intracardiac repairs, cyanotic CHD, Fontan palliation, pregnancy, and mechanical heart valves (MHV). As randomized clinical trials are lacking, most current guidelines rely on observational data and expert opinions, leading to inherent variability. While vitamin K antagonists are the only option for patients with MHV and significant mitral stenosis, direct oral anticoagulants appear to be a reasonable choice for other indications. In the presence of AA, complex conditions alone may justify anticoagulation, whereas thromboembolic and haemorrhagic risks should be evaluated individually for simpler lesions. This review summarizes the available evidence and makes relevant recommendations regarding thromboprophylaxis in ACHD patients, focusing on indications, risk scores, and therapies.