Many autistic youth have complex healthcare needs, resulting in high rates of health service utilization. However, many characteristics of this health service utilization remain unknown. Using whole-of-population data, this study aimed to quantify and compare rates of psychiatric and non-psychiatric health service utilization among autistic and non-autistic youth, with and without co-occurring intellectual disability. A national retrospective cohort study was employed using linked individual-level administrative data for Aotearoa New Zealand youth (aged 0–24 years). Health service utilization outcomes included 11 psychiatric and non-psychiatric domains. Propensity score matching on a range of sociodemographic measures compared groups across health service utilization outcomes. Data were obtained for 19,479 autistic youth, 29% of whom had a co-occurring intellectual disability and 1,561,278 non-autistic youth. Results demonstrated higher rates of mental health service utilization among autistic compared with non-autistic youth, including inpatient (prevalence ratio 5.85; 95% confidence interval 4.93–6.94) and outpatient (prevalence ratio 4.96; 95% confidence interval 4.75–5.18) service use and psychotropic medication dispensing (prevalence ratio 6.83; 95% confidence interval 6.65–7.02), particularly among autistic youth without intellectual disability. Rates of non-psychiatric hospital admissions (prevalence ratio 1.93; 95% confidence interval 1.85–2.01), potentially avoidable hospitalizations (prevalence ratio 1.91; 95% confidence interval 1.82–2.00) and outpatient visits (prevalence ratio 1.99; 95% confidence interval 1.95–2.01) were also higher among autistic youth. Research implications for delivery of healthcare services are discussed. Lay abstract Autistic youth generally use healthcare services more often than non-autistic youth. However, we know very little about the factors that can affect health service use and the types of services that are used, and this has not been explored in Aotearoa New Zealand. We analysed data from New Zealand to compare health service use among autistic and non-autistic youth (0 to 24-year-olds). Data were available for 19,479 autistic youth and 1,561,278 non-autistic youth. We compared hospitalizations, specialist visits, emergency department visits and use of different types of medications. In this study, autistic youth were found to have been hospitalized for medical and mental health reasons, more often than non-autistic youth. Autistic youth were also more likely to have attended specialist appointments and to have been given medication. These differences were particularly large for medications commonly used for mental health conditions (e.g. anxiety, depression, attention deficit hyperactivity disorder) or associated symptoms. Autistic youth who also had an intellectual disability were more likely to use healthcare services for physical health conditions, but were less likely to use mental health services, when compared with autistic youth who did not have an intellectual disability. These findings, along with other research, suggest that the healthcare needs of autistic youth are not always being met. Further work is needed to enhance our understanding of co-occurring conditions among autistic youth, including those that result in high rates of health service use, in order to inform the development of healthcare services and training for healthcare professionals to better cater to the needs of autistic youth.