This study analysed interregional migration for Indigenous patients in the Northern Territory, Australia. Individual-level linked hospitalisation data between July 1998 and June 2011 were used to describe the migration patterns and associated factors. Micro-simulations were conducted to assess the impacts on mortality estimates. Indigenous patients were 35% more likely to migrate from remote to urban areas after hospitalisation than in the reverse direction (risk ratio 1.35, 95% confidence interval 1.30-1.41). The likelihood was positively associated with hospitalisations, age and the Central Australia region. Indigenous patients with diabetes, renal disease or chronic obstructive pulmonary disease had higher risks of urban migration. Non-Indigenous patients were included for comparison. The micro-simulations indicated the patient migration may result in a 6% under-estimation of Indigenous mortality in remote and very remote areas and 3% over-estimation of mortality in urban areas. The results are pertinent to a sound understanding of health outcomes across remoteness categories.