Adverse outcomes increase in frequency as patients after Fontan operation approach adulthood. Cardiac magnetic resonance (CMR) imaging–derived parameters have been shown to predict death/transplant; however, limited data are available on the usefulness of echocardiography in risk stratification. We conducted a retrospective, single-center review of records of patients after Fontan operation with an echocardiogram and CMR within 1 year of each other. The primary end point was time to all-cause mortality or listing for transplant. Of the 127 eligible patients, there were 12 end points (9%; 10 deaths and 2 listing for transplant). Median age was 16.8 years (interquartile range 12 to 23.1) with a median follow-up of 3.8 years (interquartile range 2.6 to 5.7). Among clinical parameters, protein-losing enteropathy had the strongest association with the outcome. Among echocardiographic variables, global circumferential strain showed the strongest association (hazard ratio 1.3 per unit change, 95% confidence interval 1.1 to 1.5, p value 0.001, C-index 0.81), whereas among CMR variables indexed ventricular end-diastolic volume showed the strongest association with the outcome (hazard ratio 1.04 per 10 ml/BSA^1.3 increase in volume, 95% confidence interval 1.02 to 1.06, p value 0.001, C-index 0.82). Cox proportional hazards analysis revealed echocardiography and CMR models to each individually have a higher predictive ability than the clinical model; however, in direct comparison, neither technique was superior. In conclusion, both echocardiography-derived circumferential strain and CMR-derived ventricular end-diastolic volume index are associated with transplant-free survival in patients after Fontan operation. Echocardiography and CMR parameters have higher discriminative ability than clinical variables. Although neither imaging technique is superior in this cohort, both introduce important factors for risk stratification.