Patients with Ehlers-Danlos syndrome type IV have thin-walled, friable arteries and veins. Invasive procedures carry a significantly increased risk for perforation of blood vessels. The aim of this case report is to demonstrate the feasibility and potential benefits of using a stereotactic magnetic navigation system (MNS) for mapping and ablation under these very special circumstances. A 45-year-old woman is presented with daily episodes of typical atrio-ventricular nodal re-entry tachycardias (AVNRT) and known Ehlers-Danlos syndrome type IV. Transcatheter ablation procedure of the AVNRT was undertaken using the MNS, with a non-traumatic single floppy catheter and the capability of advanced navigation.