Reducing Indigenous overrepresentation in the criminal justice system is justified on both social justice and economic grounds. We developed an innovative costing framework and estimated direct criminal justice system unit costs based on critical cost drivers. These estimates were applied to offender trajectories, modelling offences of all individuals registered as being born in Queensland during 1983–1984 (from ages 10 to 31). Separate trajectory models were developed for Indigenous and non-Indigenous Queenslanders in the birth cohort to enable separate cost estimations for these groups. Findings identified over one-half (53%) of the identified Indigenous cohort and 16 percent of the non-Indigenous cohort had moderate to chronic offender trajectories. Because of the high levels of recontact and sanction seriousness and length, Indigenous offenders were on average more costly. These findings emphasise the high cost of current criminal justice system responses to Indigenous and chronic offenders in particular and the need to consider innovative and more cost-effective approaches to reduce offending by individuals in these groups.