Leftward posterior deviation of the atrial septum primum (LDSP) has been reported in up to 64% of patients with hypoplastic left heart syndrome (HLHS) but there are no published data on its impact on neonatal outcomes. We reviewed the prevalence of LDSP and its correlation with neonatal outcomes in our institution. This was a single-center retrospective study of neonates with HLHS from 2001 to 2019. Echocardiograms were reviewed and the presence or absence of LDSP was noted. To quantify the degree of deviation in patients with LDSP, a new measurement, the deviation index (DI) was calculated using both the subcostal long and short-axis views. Of ninety-four patients with HLHS, fifty-seven (61%) patients were noted to have LDSP. There was no statistically significant difference in gestational age (GA), birth weight (BW), or mortality between patients with and without LDSP. Patients with LDSP had an increased incidence of unplanned reoperation (p < 0.01), post-operative cardiac catheterization (p < 0.05), and post-operative infection (p < 0.05). After correction for GA, BW, HLHS subtype, and type of surgery, LDSP predicted reoperation (OR = 3.6, p < 0.01), catheterization (OR = 2.7, p = 0.05), and infection (OR = 3.4, p < 0.05). Higher degree of deviation predicted reoperation (DI > 0.17), catheterization (DI > 0.07), and infection (DI > 0.12). There was excellent inter-observer reproducibility of the DI (ICCabsolute-agreement = 0.82, ICCconsistency = 0.90). Patients with LDSP have a higher prevalence of post-operative morbidity. The degree of deviation was found to be predictive of post-operative complications. Pre-operative echocardiographic evaluation of LDSP in patients with HLHS may be helpful in risk stratification and counseling.