Abstract: Background: Government healthcare spending for Indigenous Australians is higher than for non-Indigenous Australians yet it does not appear to be impacting health outcomes equitably, especially in more remote areas. The defined region of Northern Australia is characterised by decentralised populations and has a high concentration of Indigenous people compared with southern Australia. Recent research has highlighted the need for investment in Northern Australia. The only Australian standard for economic evaluations of healthcare is the Pharmaceutical Benefits Advisory Committee (PBAC) guidelines, which recommend use of national data, such as Pharmaceutical Benefits Scheme (PBS) data. These data are more likely to be under-recorded and health services underutilised by Indigenous patients compared with non-Indigenous patients. Indigenous Australians also may have distinct health models that differ from mainstream Australian services. For these reasons, validated economic evaluation of healthcare is critical to deliver the best allocation of scarce resources for Indigenous communities in Northern Australia. Aim: This study aimed to determine how health service use and costs are captured and quantified in economic evaluations for remote and regional Indigenous populations in Northern Australia. Methods: A systematic review of health service economic evaluations involving Indigenous Australians within Northern Australia was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). A search of records published from 2010 to 2016 was conducted from PubMed, Scopus, government and non-government databases. Thematic analysis was performed on evaluations that met inclusion criteria. Results: Sixteen evaluations met the inclusion criteria from an initial 515 records identified. These studies used disparate evaluation methods. Most evaluations were performed from a state or territory perspective. Only seven evaluations captured patient data that extended outside of a state or territory source. There was no health service data capture using national data sources. Only two studies used a comprehensive societal perspective. Few studies considered Indigenous patients’ perspectives. Conclusions: Despite the needs identified for robust economic evaluations for Indigenous peoples in Northern Australia, recent evaluations have not been conducted consistently or with sufficient consideration of federal, societal and Indigenous consumer perspectives. Uncoordinated evaluations from state and territory perspectives have led to the underutilisation of established guidelines. Barriers identified, such as unlinked patient PBS data, also limit the ability of governments and researchers to conduct comprehensive economic evaluations. Methodological consistency in economic evaluations of healthcare is recommended and will lead to improved, quantifiable comparisons of health services for Indigenous patients within, and outside the health sector.