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Background Total anomalous pulmonary venous connection accompanied by unilateral lung agenesis and Goldenhar syndrome is extremely rare. Case presentation We present a case of total anomalous pulmonary venous connection accompanied by unilateral lung agenesis and Goldenhar syndrome in a patient who was diagnosed based on transthoracic echocardiography and computed tomography. We observed complete absence of the lung, the bronchial tree, and vascular structures on the right side, with abnormal drainage of the left pulmonary veins into the innominate vein. The patient showed clear clinical evidence of pulmonary venous obstruction and underwent surgery 3 days after birth. The pulmonary venous chamber containing the vertical vein was anastomosed to the left atrium using 7–0 PDS running sutures via a median sternotomy. Echocardiography and computed tomography performed 1 year postoperatively revealed no pulmonary venous obstruction. Conclusion We report a rare case of total anomalous pulmonary venous connection accompanied by unilateral lung agenesis and Goldenhar syndrome, which was successfully repaired 3 days after birth. A median sternotomy is a safe and effective approach for surgical repair of congenital heart disease with unilateral lung agenesis. Repair of the supra cardiac total anomalous pulmonary connection using the vertical vein is feasible in patients with a small pulmonary venous chamber.