Pheochromocytoma (PCC) can adversely affect Fontan circulation. However, there are few reports on its perioperative management before and after PCC resection in Fontan patients. A 24-year-old female patient with congenitally corrected transposition of the great arteries, ventricular septal defect, and pulmonary atresia who had undergone Fontan palliation developed heart failure caused by PCC. The patient was pre-conditioned for PCC resection with heart failure treatment, alpha-blocker titration, and careful infusion, and had a good intraoperative and postoperative course with no complications. Postoperative catheter data showed improvements in systemic vascular resistance, cardiac output, and central venous pressure compared with preoperative data. There is no established preconditioning method for PCC resection in patients with Fontan circulation. Careful perioperative management based on an understanding of the features of the Fontan circulation can lead to better outcomes. Pheochromocytoma (PCC) can occur in patients with Fontan circulation. Preoperative management and the PCC itself can adversely affect Fontan circulation, highlighting the importance of suspecting PCCs in Fontan patients based on symptoms such as heart failure, worsening arrhythmias, and headache, and emphasizing careful perioperative management.