The Fontan operation is performed as a palliative procedure to improve survival in infants born with a functionally univentricular circulation. The success of the operation is demonstrated by a growing adult Fontan population that exists with this unique physiology. Late follow-up has demonstrated expected and unexpected sequelae, and has shown multisystem effects of this circulation. This review discusses the challenges of managing the late complications in terms of understanding this unique physiology and the innovative therapeutic interventions that are being investigated. The challenge remains to maintain quality of life for adult survivors, as well as extending life expectancy.