Patients who undergo Fontan surgery have specific hemodynamics, wherein the systemic venous blood returns directly to the pulmonary arteries. Therefore, managing respiratory circulation in such cases is often difficult. We report a case of a pediatric patient who required tracheal intubation and was put on positive-pressure ventilation for plastic bronchitis following the Fontan procedure that disrupted the circulatory dynamics. A 7-year-old boy was admitted to the ICU for respiratory management due to worsening of oxygenation after the onset of plastic bronchitis. He underwent tracheal intubation and was placed on positive-pressure ventilation support; however, his circulatory dynamics was disrupted immediately after that. A veno venous membrane oxygenator was then used, and his oxygenation improved. A mucous plug was removed by bronchoscopy. Subsequently, ventilator management was performed, with the airway pressure reduced as much as possible, and infusion management was performed using central venous pressure as an index. Patients with Fontan circulation are at a risk of developing hemodynamic disruption with routine interventions. The number of patients with Fontan circulation is increasing as surgical outcomes improve. Therefore, it is important to understand the specific hemodynamics involved for treating such patients.