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Key Clinical Message The use of endocardial pacing in patients with univentricular hearts and intracardiac shunts is limited, primarily due to the increased risk of thromboembolism. However, when accompanied by proper long‐term anticoagulation therapy, it may be safer than epicardial interventions in selected patients at high risk for surgery. Abstract We report transvenous endocardial pacing through the atrial septal defect in a patient with tricuspid atresia, transposition of the great arteries, severe pulmonary hypertension, and complete heart block. This study is among the first reported cases using this pacing method in a patient with a univentricular heart and intracardiac shunt.