This study describes single-unit experience and explores risk stratification, with protocolised inter-stage cardiac magnetic resonance imaging for infants with hypoplastic left heart syndrome. Survival was retrospectively analysed among the cohort of locally followed survivors of Norwood Stage I procedure, who underwent magnetic resonance imaging under general anaesthesia from 2003 to 2008. This included 32 patients: 17 with Sano conduit and 15 with arterio-pulmonary shunt. The median (inter-quartile range) age and weight at scan were 3.1 (2.6–4.6) months and 5.0 (4.5–5.3) kilograms, respectively. Using morphologic definitions, the median coarctation index was 0.71 (0.57–0.83). The degree of proximal right and left pulmonary artery narrowing was 25% (14–44%) and 25% (11–50%), respectively. The median right ventricular ejection fraction was 54% (48–59%). The ejection fraction was not related to the coarctation index or to pulmonary artery narrowing. Patients were followed up for a median of 19.2 (10.8–46.0) months, during which 13 (41%) had an intervention in addition to routine Norwood Stage II surgery and seven died. Risk of death was related to reduced right ventricular ejection fraction, with a hazard ratio of 0.91 (95% confidence interval 0.85–0.98, p = 0.02), and the cumulative number of focal stenoses of neo-aortic arch and pulmonary arteries (hazard ratio 2.71, 95% confidence interval 1.14–6.44, p = 0.02). Conclusions: In addition to comprehensive three-dimensional morphologic imaging, inter-stage cardiac magnetic resonance imaging provides a ventricular functional index that may predict outcome in patients with hypoplastic left heart syndrome. Measures to preserve right ventricular systolic function and relieve stenoses are paramount within the complex management strategies for these patients.