Besides antiarrhythmic medication, there are now very good options for a potentially curative therapy by catheter ablation targeting the origin of the underlying arrhythmias in patients with complex congenital heart disease. Three-dimensional (3D) reconstruction of tomographic imaging (MRI or computed tomography) is helpful to understand the underlying cardiac anatomy, identify the most likely target chamber, and help with planning access. Use of the available 3D mapping systems (sequential or simultaneous acquisition) and (if available) more advanced navigation systems, such as remote magnetic navigation, can improve the acute and long-term outcomes of catheter ablation in congenital heart disease.