Systemic ventricular end-diastolic pressure (SVEDP) is an important determinant of pulmonary artery pressure in those with a Fontan circulation. Predictors of an elevated SVEDP have been incompletely identified in this population. All who underwent the Fontan operation at our center between 1/2009 and 12/2013 were retrospectively identified. SVEDP at the pre-Fontan catheterization and other patient variables were extracted. We identified 61 patients. Pre-Fontan SVEDP was positively associated with systemic ventricular systolic pressure (β = 0.4, p = 0.004), aortic systolic pressure (β = 0.3, p = 0.007), aortic mean pressure (β = 0.3, p = 0.02), and decreased ventricular systolic function (p = 0.03). Compared to those with pre-Fontan SVEDP ≤ 7 mmHg, patients with SVEDP > 7 mmHg had higher average ventricular systolic pressure (85.0 ± 7.5 vs. 78.7 ± 8.3 mmHg, p = 0.003), higher average descending aorta mean pressure (62.4 ± 4.9 vs. 58.6 ± 8.1 mmHg, p = 0.03), and a higher incidence of decreased ventricular systolic function (36 vs. 15%, p = 0.07). For those with a systemic right ventricle, the SVEDP decreased significantly from the pre-Stage 2 to pre-Fontan measurements (8.7 ± 2.6 vs. 7.3 ± 2.0 mmHg, p = 0.02), but not for those with a systemic left ventricle (7.8 ± 2.0 vs. 7.2 ± 1.8 mmHg, p = 0.3). At pre-Fontan catheterization, decreased ventricular systolic function and markers of systemic afterload were positively associated with the SVEDP. SVEDP decreased significantly after Stage 2 for those with a systemic right ventricle, but not for those with a systemic left ventricle; the systemic right ventricle may be particularly vulnerable to pre-Stage 2 volume loading.