Cystic tumor of the atrioventricular nodal region is a rare cardiac primary tumor that can cause heart blockage and sudden death. Antemortem diagnosis and successful excision of the atrioventricular nodal region are extremely rare. A 45-year-old woman who presented with palpitations is reported. Electrocardiography revealed first-degree atrioventricular block. Echocardiography, computed tomography, and magnetic resonance imaging scans revealed a cystic mass attached to the interatrial septum. Complete surgical excision of the mass was achieved, although placement of a permanent pacemaker was required for complete heart blockage. Histopathological examination revealed the mass to be a cystic tumor of the atrioventricular nodal region. A 5-year follow-up has revealed no sign of recurrence.