Novel commercially available software has enabled registration of both CT and MRI images to rapidly fuse with X-ray fluoroscopic imaging. We describe our initial experience performing cardiac catheterisations with the guidance of 3D imaging overlay using the VesselNavigator system (Philips Healthcare, Best, NL). A total of 33 patients with CHD were included in our study. Demographic, advanced imaging, and catheterisation data were collected between 1 December, 2016 and 31 January, 2019. We report successful use of this technology in both diagnostic and interventional cases such as placing stents and percutaneous valves, performing angioplasties, occlusion of collaterals, and guidance for lymphatic interventions. In addition, radiation exposure was markedly decreased when comparing our 10–15-year-old coarctation of the aorta stent angioplasty cohort to cases without the use of overlay technology and the most recently published national radiation dose benchmarks. No complications were encountered due to the application of overlay technology. 3D CT or MRI overlay for CHD intervention with rapid registration is feasible and aids decisions regarding access and planned angiographic angles. Operators found intraprocedural overlay fusion registration using placed vessel guidewires to be more accurate than attempts using bony structures.