When addressing disparities in health status of Indigenous Australians, it is necessary to consult with Indigenous people to explore their health needs. The process of improving health outcomes is complex; it requires acknowledgement of underlying cultural and social determinants of health and active engagement of Indigenous people to define the issues and identify solutions. The aim of this study is to explore the most appropriate research methodologies to determine Australian Indigenous community members’ perceptions of their health needs. A scoping review was conducted in BioMed Central, CINAHL, Informit Health, MEDLINE Ovid, ProQuest and Scopus databases and Google Scholar for all relevant literature published between 2009 and 2018. Extensive manual searches of reference lists were also undertaken. The limited number of articles relating to needs assessment with Indigenous community members prescribed broadening the scope of the review to include articles that describe methodologies to enhance Indigenous people’s engagement in the research process. Twelve papers met the inclusion criteria. Three major themes emerged: (1) the imperative to develop and implement Indigenist research methodologies; (2) participatory action research (PAR) and community-based participatory research (CBPR) as appropriate methodologies to conduct research with Indigenous community members; and (3) yarning or storytelling as a culturally appropriate Indigenous method of data collection.