Protein-losing enteropathy (PLE) is a severe Fontan complication. This is a case report of the first hybrid treatment of PLE in Denmark of an 11-year-old Fontan patient with severe symptoms (diarrhoea, fatigue and swelling) and low albumin level. Diagnostics included intranodal and intrahepatic dynamic contrast magnetic resonance lymphangiography. The hybrid intervention consisted of selective lymphatic duct embolisation and innominate vein turn-down to treat PLE. The interventions went well, and two months after discharge the patient was relieved from PLE symptoms, the albumin level was normalised, and the patient felt more energetic.