Neo-aortic arch obstruction (NAAO) is a common complication following the Norwood/Sano procedure (NP) for hypoplastic left heart syndrome (HLHS) and is associated with increased morbidity and mortality. However, there is currently no objective method for predicting which patients will develop NAAO. This study was designed to test the hypothesis that hemodynamic changes from development of NAAO after NP in patients with HLHS will lead to changes in myocardial dynamics that could be detected before clinical symptoms develop with strain analysis using velocity vector imaging. Patients with HLHS who had at least one cardiac catheterization after NP were identified retrospectively. Strain analysis was performed on all echocardiograms preceding the first catheterization and any subsequent catheterization performed for intervention on NAAO. Twelve patients developed NAAO and 30 patients never developed NAAO. Right ventricular strain was worse in the group that developed NAAO (−6.2 vs. −8.6 %, p = 0.040) at a median of 59 days prior to diagnosis of NAAO. Those patients that developed NAAO following NP were significantly younger at the time of first catheterization than those that did not develop NAAO (92 ± 50 vs. 140 ± 36 days, p = 0.001). This study demonstrates that right ventricular GLS is abnormal in HLHS patients following NP and worsening right ventricular strain may be predictive of the future development of NAAO.