Background <p>Pneumoperitoneum and Trendelenburg positioning are thought to increase pulmonary vascular resistance (PVR). In Fontan circulation, increased PVR is directly related to decreased ventricular preload and can result in circulatory failure.</p> Case presentation <p>A 23-year-old female patient with Fontan physiology was diagnosed with left paraovarian cyst torsion and underwent laparoscopic cystectomy. SpO₂ was 70% in room air. General anesthesia was induced with remimazolam, fentanyl, and rocuronium and maintained with remimazolam and remifentanil combined with an abdominal wall block. The difference between SpO₂ and central venous oxygen saturation (ScvO₂) increased during the induction of anesthesia and further increased with the initiation of pneumoperitoneum and Trendelenburg positioning but recovered at the completion of the surgery.</p> Conclusions <p>Patients with Fontan physiology and severe hypoxemia can tolerate short-term laparoscopic surgery in the Trendelenburg position under strict management. In these patients, monitoring ScvO₂ provides important circulatory information regarding the effects of pneumoperitoneum and Trendelenburg positioning.</p>