Background To determine (1) correlation between Doppler stroke volume index (SVI) and cardiac magnetic resonance imaging (CMRI) SVI and (2) association between Doppler SVI and Fontan-associated diseases (FAD) and Fontan failure. Methods Review of Fontan patients who underwent same-day CMRI and transthoracic echocardiography (TTE), 2005 to 2015. We defined FAD as cardiac thrombus, protein-losing enteropathy, arrhythmia, and hospitalization for heart failure. Fontan failure was defined as Fontan conversion or revision, heart transplantation or listing, or death. Results Fifty-three patients with systemic left ventricle (LV) underwent 86 sets of TTE/CMRI. Mean (SD) age 31 (6) years. SVI (45  vs 42  mL/m2), CI (3.0 [1.1] vs 2.8 [0.8] L min−1 m−2), and ejection fraction (53 % vs 51 %) were similar for both modalities (P >.05 for all). Doppler SVI correlated with CMRI (r = 0.68; P <.001). Sixteen patients had cirrhosis, and these patients had a higher CI (3.9 [0.9] vs 2.8 [1.0] L min−1 m−2; P <.01). Among the 37 patients without cirrhosis, Doppler SVI <39 mL/m2 was associated with FAD (odds ratio [OR], 2.11; 95% confidence limit, 1.26–3.14; P =.02); Fontan failure was more common in patients with CI was <2.5 L min−1 m−2 (3/9 [33%] vs 0/28 [0%], P =.01). Another 11 patients with systemic right ventricle (RV) underwent 17 sets of TTE/CMRI, mean (SD) age 17 (3) years, and CMRI SVI also correlated with Doppler SVI (r = 0.75; P <.001). Conclusion Doppler SVI correlated with CMRI SVI in patients with systemic LV and systemic RV. The association between output measures (SVI and CI) and FAD were seen only in single LV patients (single RV patients not assessed for this outcome due to small numbers). An association between low Doppler CI and Fontan failure was suggested in a small number of single LV patients.