Background Patients with a single ventricle who experience early life growth failure suffer high morbidity and mortality in the perisurgical period. However, long-term implications of poor infant growth, as well as associations between body mass index (BMI) and outcome in adulthood, remain unclear. We aimed to model BMI trajectories of patients with a single ventricle undergoing a Fontan procedure to determine trajectory-based differences in baseline characteristics and long-term clinical outcomes. Methods and Results We performed a retrospective analysis of medical records from patients in the Australia and New Zealand Fontan Registry receiving treatment at the Royal Children's Hospital, The Children's Hospital at Westmead, Royal Melbourne Hospital, and Royal Prince Alfred Hospital from 1981 to 2018. BMI trajectories were modeled in 496 patients using latent class growth analysis from 0 to 6 months, 6 to 60 months, and 5 to 16 years. Trajectories were compared regarding long-term incidence of severe Fontan failure (defined as mortality, heart transplantation, Fontan takedown, or New York Heart Association class III/IV heart failure). Three trajectories were found for male and female subjects at each age group-lower, middle, higher. Subjects in the lower trajectory at 0 to 6 months were more likely to have an atriopulmonary Fontan and experienced increased mortality long term. No association was found between higher BMI trajectory, current BMI, and long-term outcome. Conclusions Poor growth in early life correlates with increased long-term severe Fontan failure. Delineation of distinct BMI trajectories can be used in larger and older cohorts to find optimal BMI targets for patient outcome.