The effects of the nondominant or secondary ventricle on the Fontan circulation are not known. The present study used cardiac magnetic resonance imaging to investigate the relations between secondary ventricular size and global cardiac performance. The Fontan cross-sectional study collected data from 7 centers participating in the Pediatric Heart Network. Subjects with complete cardiac magnetic resonance imaging data and an identifiable secondary ventricle were included in the analysis. Relationships between body surface area-adjusted parameters of the secondary ventricle (mass, end-diastolic volume, mass/volume ratio, and stroke volume) and the following measures were assessed. These measures included the percentage of predicted peak oxygen consumption and oxygen consumption at the ventilatory anaerobic threshold, ejection fraction of the main ventricular chamber, echocardiographic diastolic function grade, serum B-type natriuretic peptide, primary ventricular end-diastolic pressure, and parent-reported physical functioning summary score on the Child Health Questionnaire. Of the 546 enrolled subjects, 123 (age 12.1 ± 3.3 years, 56% male) had undergone cardiac magnetic resonance imaging, and 38 had achieved maximal aerobic capacity. A larger secondary ventricular end-diastolic volume, lower mass/volume ratio, and greater secondary/total ventricular stroke volume ratio were associated with a greater exercise capacity. No significant relationships were found between the measures of the secondary ventricle and the other outcomes. In conclusion, in children after the Fontan operation, a larger and less hypertrophied secondary ventricle with a greater contribution to stroke volume was associated with a better exercise capacity.