Objective: To estimate the lifetime health costs of stroke by comorbidity and indigenous status in Australia's Northern Territory (NT), where a large indigenous population resides. Methods: Incidence-based cohort study using linked hospital, primary care, and Pharmaceutical Benefits Scheme data to estimate lifetime direct costs for hemorrhagic stroke (HS), ischemic stroke (IS) and undetermined stroke (UND). Inverse probability-weighted survival analysis was adapted to adjust for loss to follow-up. Log-linear modeling was used to analyze the net stroke costs and marginal comorbidity costs by indigenous status. Results: Between 1992 and 2013, there were 3,733 patients admitted with stroke in the NT (74% were incident strokes, 38% indigenous, 56% male, 56% IS). In 2012/2013 Australian dollars, the estimated lifetime cost for an incident stroke in NT was $302,538 AUD ($207,218 USD) per patient. The net lifetime cost per non-indigenous female HS patient aged <45 years without comorbidity (reference category) was $72,773 AUD ($49,844 USD); IS cost 54% and UND 9% more than HS (p < 0.01). Stroke cost was greater for indigenous patients (Δ 44%) and patients with renal disease (Δ 71%), coronary heart disease (Δ 44%), hypertension (Δ 30%), and diabetes (Δ 28%) in comparison with the reference category (all p < 0.01). Chronic obstructive pulmonary disease, atrial fibrillation, depression, and cancer were negatively associated with lifetime stroke costs. Conclusions: The costs of stroke for indigenous people and patients with different comorbidities are substantial and an integrated prevention strategy is needed.