One-third of Australia’s Aboriginal and Torres Strait Islander population are adolescents. Recent data highlight their health needs are substantial and poorly met by existing services. To design effective models of primary healthcare, we need to understand the enablers and barriers to care for Aboriginal and Torres Strait Islander adolescents, the focus of this study. This protocol was codesigned with Apunipima Cape York Health Council that supports the delivery of primary healthcare for 11 communities in Far North Queensland. We framed our study around the WHO global standards for high-quality health services for adolescents, adding an additional standard around culturally safe care. The study is participatory and mixed methods in design and builds on the recommended WHO assessment tools. Formative qualitative research with young people and their communities (exploring concepts in the WHO recommended quantitative surveys) seeks to understand demand-side enablers and barriers to care, as well as preferences for an enhanced response. Supply-side enablers and barriers will be explored through: a retrospective audit of clinic data (to identify current reasons for access and what can be strengthened); an objective assessment of the adolescent friendliness of clinical spaces; anonymous feedback from adolescent clients around quality of care received and what can be improved; and surveys and qualitative interviews with health providers to understand their perspectives and needs to provide enhanced care. This codesigned project has been approved by Apunipima Cape York Health Council and Far North Queensland Human Research Ethics Committee. The findings from this project will inform a codesigned accessible and responsive model of primary healthcare for Aboriginal and Torres Strait Islander adolescents.