BackgroundDespite advances in neonatal intensive care, babies admitted to Neonatal Intensive Care Units (NICU) suffer from adverse outcomes. We aim to describe the longer-term respiratory infectious morbidity of infants discharged from NICU using state-wide population-based linked data in Western Australia.Study designWe used probabilistically linked population-based administrative data to analyse respiratory infection morbidity in a cohort of 23,784 infants admitted to the sole tertiary NICU, born 2002–2013 with follow up to 2015. We analysed incidence rates of secondary care episodes (emergency department presentations and hospitalisations) by acute respiratory infection (ARI) diagnosis, age, gestational age and presence of chronic lung disease (CLD). Poisson regression was used to investigate the differences in rates of ARI hospital admission between gestational age groups and those with CLD, after adjusting for age at hospital admission.ResultsFrom 177,367 child-years at risk (i.e., time that a child could experience an ARI outcome), the overall ARI hospitalisation rate for infants and children aged 0–8 years was 71.4/1000 (95% confidence interval, CI: 70.1, 72.6), with the highest rates in infants aged 0–5 months (242.9/1000). For ARI presentations to emergency departments, equivalent rates were 114/1000 (95% CI: 112.4, 115.5) and 337.6/1000, respectively. Bronchiolitis was the most common diagnosis among both types of secondary care, followed by upper respiratory tract infections. Extremely preterm infants (< 28 weeks gestation at birth) were 6.5 (95% CI: 6.0, 7.0) times more likely and those with CLD were 5.0 (95% CI: 4.7, 5.4) times more likely to be subsequently admitted for ARI than those in NICU who were not preterm or had CLD after adjusting for age at hospital admission.ConclusionsThere is an ongoing burden of ARI in children who graduate from the NICU, especially those born extremely preterm, that persists into early childhood. Early life interventions to prevent respiratory infections in these children and understanding the lifelong impact of early ARI on later lung health are urgent priorities.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12887-023-04152-5.