A child with early failure of a Fontan circulation was listed for cardiac transplantation and then developed a subhepatic abscess. Surgical drainage was deemed necessary after the failure of an attempted percutaneous procedure. Following a multidisciplinary discussion, a laparoscopic technique was chosen to optimise postoperative recovery. To our knowledge, the literature does not describe any case of laparoscopic surgery in a patient with a failing Fontan circulation. This case report highlights the physiological variations involved with this management strategy, discusses the implications and risks, and offers some recommendations.