Transcatheter creation or enlargement of an atrial septal defect has been used to promote adequate blood flow and mixing in some forms of congenital heart defects or as a relief valve in right or left atrial hypertension, resulting in better cardiac output and/or systemic saturation. We report a case of a 4-year-old male affected by complex congenital heart disease who was admitted for management of severe cyanosis following a staged pericardial fenestrated Fontan procedure. Transoesophageal echocardiogram showed a wide fenestration of 9 mm in size with a severely dilated pericardial Fontan system. To avoid a new surgical procedure and as part of a compassionate use programme, we decided to implant an atrial flow regulator device (4 mm in diameter) with percutaneous approach with the goal of reducing the right-to-left shunt and increasing the pulmonary flow. Preprocedural oxygen saturation was 75%, whereas after 2 months of follow-up, we observed a progressive increase of up to 95% with significant reduction in the pericardial Fontan system dimensions at echocardiography.