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Introduction Following the Fontan procedure, children require lifelong anticoagulant therapy to minimise the risk of thrombosis. Factors influencing the management of warfarin therapy in children post-Fontan procedure are poorly understood. This study investigated factors affecting warfarin therapy stability and time to reach target therapeutic range, in children post-Fontan procedure. Materials and Methods Medical histories of children who had undergone Fontan procedures between 1st June 2008 and 1st June 2010 were retrospectively audited. Variables of interest included dietary intake, activity level, gastro-intestinal function, presence of intercostal catheters and antibiotic therapy requirements. Time of warfarin commencement, attainment of a therapeutic International Normalized Ratio (INR) and dosing of warfarin were of particular interest. Results Decreased warfarin dosage, compared to the clinical practice guidelines, was seen in all children. Antibiotic requirement correlated with an increased hospital length of stay in post-Fontan patients. Requirement for maintenance fluids and immobility lead to a further decrease in the warfarin dose received. Conclusions This study presents previously unknown information about the trajectory of warfarin therapy in children post-Fontan procedure. Results contribute to our understanding of the factors that impact warfarin stability in this population. This evidence together with continued research may aid to improve the clinical management of children post-Fontan procedure by reducing the time required to attain target INRs and, potentially length of hospital stay.