Aim: Chronic health conditions are associated with poor academic outcomes. This study examines the relationship between health conditions, specialist health service utilisation and academic performance in Australian children. Methods: This was a quasi-longitudinal study where School Entrant Health Questionnaire (a survey tool with parent report on children's health) data for 24 678 children entering school in 2008 was matched with the 2011 National Assessment Program - Literacy and Numeracy (NAPLAN). Linear and logistic regressions were used to examine associations between health conditions, use of a specialist health service and reading and numeracy scores. Results: The study comprised 24 678 children. Children with allergies, very low birth weight, developmental delay, diabetes, spina bifida, cystic fibrosis, birth abnormality, speech problems, intellectual disability and attention-deficit/hyperactivity disorder had lower numeracy scores than those without any of these conditions (P < 0.05). The same children had higher odds (1.2-5.8) of being at or below the national minimum standard for numeracy. Children with developmental delay, epilepsy, dental problems, speech, intellectual disabilities and low birth weight had lower reading scores than those without these conditions (P < 0.05) and had higher odds of being at (odds ratio: 1.3) or below (odds ratio: 3.7) the national minimum standard for reading. Children with health conditions who had ever accessed specialist health services did not differ in their academic performance from those that had not used specialist health services. Conclusions: Some health conditions put children at risk of poorer academic performance, and interventions to prevent this such as appropriate support services in schools should be considered.