OBJECTIVE: To report the comparative rates, average length of stay and cost per episode of hospital management for self-harm in three age cohorts: 15-19 years, 20-24 years and 25-29 years; by sex and indigeneity. DESIGN, SETTING, PARTICIPANTS: A secondary data analysis of the Australian Institute of Health and Welfare (AIHW) dataset between 1st January 2014 and 31st December 2014 inclusive. MAIN OUTCOME MEASURES: Cost per episode of hospitalised self-harm and rates by age group, sex and Indigenous status. RESULTS: The rate of hospitalised self-harm among Australian youth was 254.0 per 100,000 population. This rate resulted in an annual cost to the healthcare system of AU$55 million or an average cost per episode of $4649 (95% CI $4488:$4810). Hospitalised self-harm was 21 times higher than the rate of suicide (11,820 episodes of hospitalised self-harm/564 suicides). Indigenous youth had on average a 1.4 times higher rate of hospitalised self-harm and 2.2 times higher rate of suicide than non-Indigenous counterparts. When controlling for age and sex, the average cost per episode was significantly lower for Indigenous youth compared to non-Indigenous youth, estimated marginal means $4538 and $4954, respectively (p < 0.001). CONCLUSIONS: Hospitalised self-harm among Australian youth resulted in a substantial cost to the healthcare system. This cost is only part of the overall burden associated with self-harm. The rate of hospitalised self-harm was significantly higher in Indigenous youth, but the associated cost per episode was significantly lower.