We present a case report on anesthesia management for a 16-year-old male with Fontan circulation undergoing pacemaker implantation, necessitating one-lung ventilation. The patient had a complex congenital heart condition and had previously undergone multiple surgeries, including a Fontan procedure. Due to his unique cardiovascular anatomy, a left thoracotomy was chosen for pacemaker implantation, which required one-lung ventilation for surgical approach and visualization. This procedure can pose significant risks in patients with Fontan circulation due to potential intraoperative increases in pulmonary vascular resistance, which is notoriously difficult to manage in the acute setting. Preoperative assessments showed that the patient had good exercise tolerance, preserved biventricular contractility, and normal liver and kidney function. However, he had a slightly elevated central venous pressure. We employed a meticulous anesthetic plan to minimize the risks associated with one-lung ventilation. This included inserting pre-induction arterial and central venous catheters, using total intravenous anesthesia with propofol and remifentanil, and administering circulatory support agents, such as dobutamine and norepinephrine. Arterial blood and central venous pressure were closely monitored throughout the procedure. Further, cardiac activity was monitored using transesophageal echocardiography (TEE). The patient's hemodynamic stability was maintained intraoperatively, and the pacemaker lead was successfully implanted without significant complications. Postoperatively, we administered continuous intravenous fentanyl infusion and intercostal nerve blocks for pain control. He had an uneventful recovery and was discharged from the intensive care unit the day after surgery. This case contributes to the limited but growing body of literature on anesthesia management in patients with Fontan circulation, particularly related to the use of one-lung ventilation, and appropriate selection of anesthetic agents and circulatory support drugs. Further research is necessary to establish best practices and improve surgical outcomes in these patients.