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 41-year-old woman who presented with dyspnea and palpitations is reported. Electrocardiography revealed third-degree atrioventricular block. Echocardiography showed a right atrial cystic mass attached to the interatrial septum. The patient underwent surgical excision of the mass. Histopathological findings were of a cystic tumor of the atrioventricular nodal region. Placement of a permanent pacemaker was required for complete heart blockage. A two-year follow-up has revealed no sign of recurrence. This is the first case to be reported in China.