ObjectiveTo examine academic outcomes among children hospitalised with a chronic health condition.DesignPopulation-level birth cohort.SettingNew South Wales, Australia.Participants397 169 children born 2000–2006 followed up to 2014.Intervention/exposureHospitalisations with a chronic condition.Main outcome measuresAcademic underperformance was identified as ‘below the national minimum standard’ (BNMS) in five literacy/numeracy domains using the national assessment (National Assessment Program-Literacy and Numeracy) data. Multivariable logistic regression assessed the adjusted ORs (aORs) of children performing BNMS in each domain at each grade (grades 3, 5 and 7, respectively).ResultsOf children hospitalised with a chronic condition prior to National Assessment Program-Literacy and Numeracy (NAPLAN) (16%–18%), 9%–12% missed ≥1 test, with a maximum of 37% of those hospitalised ≥7 times, compared with 4%–5% of children not hospitalised. Excluding children who missed a NAPLAN test, more children hospitalised with a chronic condition performed BNMS across all domains and grades, compared with children not hospitalised (eg, for BNMS in reading at grade 3: n=2588, aOR 1.35 (95% CI 1.28 to 1.42); for BNMS in numeracy at grade 3: n=2619, aOR 1.51 (95% CI 1.43 to 1.59)). Increasing frequency and bed-days of hospitalisation were associated with 2–3 fold increased odds of performing BNMS across all domains and grades. Children hospitalised with mental health/behavioural conditions had the highest odds of performing BNMS across all domains at each grade.ConclusionsChildren hospitalised with a chronic condition underperform academically across literacy/numeracy domains at each school grade. Health and educational supports are needed to improve these children’s academic outcomes.