Arrhythmias in patients with congenital heart disease present a challenge to the care of these patients and can result in significant morbidity and mortality. Transposition of the great arteries and common arterial trunk are no exceptions. It is important to identify risk factors for arrhythmia development in the peri-operative period. The peri-operative arrhythmia burden may relate to the underlying congenital heart disease, haemodynamic perturbations, operative events, and potential residual lesions. In addition, these patients are at risk for developing arrhythmias later in life, and non-invasive and potentially invasive arrhythmia surveillance should be a routine part of the care of these patients. This article highlights important strategies to manage arrhythmia development and prevention in this patient population.