Patients with hypoplastic left heart syndrome (HLHS) are now surviving through to Fontan palliation and beyond, however, with increased morbidity and mortality. Prolonged QRSd has become one of the predictors of morbidity and mortality in certain congenital heart diseases. There is limited data characterizing the QRSd in patients with HLHS. We aimed to describe the changes in QRSd at various times during the lifetime and to evaluate whether QRSd correlates with a higher risk of developing a composite endpoint of heart failure, heart transplant, or death. We conducted a retrospective chart review of patients with HLHS who survived Fontan palliation. QRSd was measured on ECGs at various stages pre- and postsurgical palliations and subsequently at 5 year intervals. Patients with a composite endpoint were compared to those without. A total of 89 patients were included in the final analysis. The QRSd increased significantly with time from 68.7 ± 9.0 ms prior to Norwood to 91.0 ± 14.0 ms immediately following Fontan and 104.7 ± 13.6 ms 15 years after Fontan (p < 0.001). The composite endpoint was observed in 28 patients (31.4%). The time trends of QRSd differ so that the patients having the composite endpoint experienced a greater increase in QRSd over time (p = 0.009). Ever having a QRSd of 120 ms or more predicted the composite endpoint with 93% specificity. The area under the curve of the receiver operator curve analysis was 0.596. A Cox regression analysis demonstrated that QRS duration > 120 ms was independently related to a greater frequency of composite endpoint and this was confirmed by a Kaplan–Meier analysis (p = 0.011). This study unveils a novel relationship between QRSd of 120 ms or more with the composite endpoint. Despite the low sensitivity, this finding on a routine surveillance ECG could help identify HLHS Fontan patients at risk for heart failure, heart transplant, or death.