Hospital-treated self-harm rates for Aboriginal and Torres Strait Islander (Indigenous) people are at least double those for other Australians. Despite this, limited research has explored the relationship between Indigeneity and the clinical management of hospital-treated deliberate self-harm. A retrospective clinical cohort study (2003–2012) at a regional referral centre (NSW) for deliberate self-poisoning was used to explore the magnitude and direction of the relationship between Indigeneity and discharge destination (psychiatric hospital vs. other) using a series of logistic regressions. There were 149 (4%) Indigenous and 3697 (96%) non-Indigenous deliberate self-poisoning admissions during the study period. One-third (31%) were referred to the psychiatric hospital at discharge; Indigenous 21% (n = 32) vs. non-Indigenous 32% (n = 1175). Those who identified as Indigenous were less likely to be discharged to the psychiatric hospital, OR 0.59 (0.40–0.87) at the univariate level, with little change after sequential adjustment; and AOR 0.34 (0.21–0.73) in the fully adjusted model. The Indigenous cohort had a lower likelihood of psychiatric hospital discharge even after adjustment for variables associated with discharge to the psychiatric hospital highlighting the need for further investigation of the reasons accounting for this differential pattern of clinical management and the effectiveness of differential after-care allocation.