Objective: Symptomatic neonates with Ebstein’s anomaly pose significant challenge. Within this cohort, neonates with associated anatomical pulmonary atresia have higher mortality. We review our experience with this difficult subset. Methods: A total of 32 consecutive symptomatic neonates with Ebstein’s anomaly underwent surgical intervention between 1994 and 2013. Of them, 20 neonates (62%, 20/32) had associated pulmonary atresia. Patients’ weights ranged from 1.9 to 3.4 kg. All patients without pulmonary atresia had two-ventricle repair. Of the 20 neonates, 16 (80%, 16/20) with Ebstein’s anomaly and pulmonary atresia had two-ventricle repair and 4 had single-ventricle palliation, of which 2 underwent Starnes’ palliation and 2 Blalock–Taussig shunts. Six recent patients with Ebstein’s anomaly and pulmonary atresia had right ventricle to pulmonary artery valved conduit as part of their two-ventricle repair. Results: Overall early mortality was 28% (9/32). For those without pulmonary atresia, mortality was 8.3% (1/12). For the entire cohort of neonates with Ebstein’s anomaly and pulmonary atresia, mortality was 40% (8/20; p=0.05). Mortality for neonates with Ebstein’s anomaly and pulmonary atresia having two-ventricle repair was 44% (7/16). Mortality for neonates with Ebstein’s anomaly and pulmonary atresia having two-ventricle repair utilising right ventricle to pulmonary artery conduit was 16% (1/6). For those having one-ventricle repair, the mortality was 25% (1/4). Conclusions: Surgical management of neonates with Ebstein’s anomaly remains challenging. For neonates with Ebstein’s anomaly and anatomical pulmonary atresia, single-ventricle palliation is associated with lower early mortality compared with two-ventricle repair. This outcome advantage is negated by inclusion of right ventricle to pulmonary artery conduit as part of the two-ventricle repair.