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ObjectiveGiven the paucity of long-term outcome data for complex congenital heart disease (CHD), we aimed to describe the treatment pathways and survival for patients who started interventions for functionally univentricular heart (FUH) conditions, excluding hypoplastic left heart syndrome.MethodsWe performed a retrospective cohort study using all procedure records from the National Congenital Heart Diseases Audit for children born in 2000–2018. The primary outcome was mortality, ascertained from the Office for National Statistics in 2020.ResultsOf 53 615 patients, 1557 had FUH: 55.9% were boys and 67.4% were of White ethnic groups. The largest diagnostic categories were tricuspid atresia (28.9%), double inlet left ventricle (21.0%) and unbalanced atrioventricular septal defect (AVSD) (15.2%). The ages at staged surgery were: initial palliation 11.5 (IQR 5.5–43.5) days, cavopulmonary shunt 9.2 (IQR 6.0–17.1) months and Fontan 56.2 (IQR 45.5–70.3) months. The median follow-up time was 10.8 (IQR 7.0–14.9) years and the 1, 5 and 10-year survival rates after initial palliation were 83.6% (95% CI 81.7% to 85.4%), 79.4% (95% CI 77.3% to 81.4%) and 77.2% (95% CI 75.0% to 79.2%), respectively. Higher hazards were present for unbalanced AVSD HR 2.75 (95% CI 1.82 to 4.17), atrial isomerism HR 1.75 (95% CI 1.14 to 2.70) and low weight HR 1.65 (95% CI 1.13 to 2.41), critical illness HR 2.30 (95% CI 1.67 to 3.18) or acquired comorbidities HR 2.71 (95% CI 1.82 to 4.04) at initial palliation.ConclusionAlthough treatment pathways for FUH are complex and variable, nearly 8 out of 10 children survived to 10 years. Longer-term analyses of outcome based on diagnosis (rather than procedure) can inform parents, patients and clinicians, driving practice improvements for complex CHD.