Fontan palliation patients are at risk for ventricular arrhythmias post-operatively. This study aimed to evaluate whether differences in the spatial QRS-T angle can reliably predict ventricular arrhythmias in patients who had undergone Fontan palliation. A total of 117 patients who had the Fontan palliation and post-Fontan catheterization were included. Ventricular arrhythmias were identified in nine patients. Measurements of ECG parameters including QRS vector magnitude, QRS duration, corrected QT interval, and spatial peaks QRS-T angles were performed, and compared between those with and without ventricular arrhythmias. The only ECG parameter to distinguish those with versus those without VA was the SPQRS-T angle (p < 0.001), which at a cut-off value of 102.9° gave sensitivity, specificity, positive and negative predictive values of 100.0, 57.0, 17.6 and 100.0%, respectively. Only the spatial peaks QRS-T angle differentiated those with and without ventricular arrhythmia development with a univariate HR 1.237 (95% CI 1.021–1.500) and a multivariate HR of 1.032 (1.009–1.056) when catheter measured parameters were taken into account. In Fontan patients, the spatial peaks QRS-T angle is a significant independent predictor of ventricular arrhythmias. Clinical usefulness of this parameter remains to be seen and should be tested prospectively.