The prognostic factors in patients with biventricular heart who underwent Fontan surgery remain unclear. This study wanted to assess the hypothesis that interventricular dyssynchrony evaluated by cardiac magnetic resonance imaging (MRI) can predict future cardiac events in patients with biventricular heart who have undergone Fontan surgery. We prospectively enrolled consecutive patients with biventricular Fontan circulation from 2003 to 2016, and performed protocolized cardiac MRI. We determined the stroke volume ratio (SVr) using the following formula to assess interventricular dyssynchrony: (stroke volume (SV) of the two whole ventricles)/(SV of the right ventricle + SV of the left ventricle), by tracing cine MRI data. If interventricular dyssynchrony existed, blood flowed and returned to each ventricle through the ventricular septal defect; therefore, the SVr in this instance should be less than 1.0. We enrolled 40 patients. SVr ranged from 0.81 to 1.0 (median 0.95). Low SVr (< 0.95) was associated with worse New York Heart Association functional class, longer QRS duration, right bundle branch block, low biventricular indexed stroke volume, and low biventricular ejection fraction. During the follow-up period (median 53.5 months), 10 cardiac events occurred (six cases of acute exacerbation of heart failure, three cases of supraventricular tachycardia, and one case of exacerbation of protein-losing enteropathy). Univariate analysis showed four clinical predictors: SVr < 0.95 [hazard ratio (HR) 9.3, 95% confidential interval (CI) 1.7–171.5]; biventricular ejection fraction < 0.45 (HR 9.4, 95% CI 2.2–65.3); left ventricular indexed end-diastolic volume > 73 mL/m² (HR 4.5, 95% CI 1.1–15.7); and the presence of the aorta directly arising from the right ventricular conus (HR 5.8, 95% CI 1.1–106). SVr derived from MRI can predict future cardiac events in Fontan patients with biventricular hearts.