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Introduction LGBTQ+ young people in rural Australia face significant health challenges due to stigma, discrimination and structural barriers that hinder effective access to care. The inaccessibility or altogether absence of tailored primary healthcare services exacerbates poor health outcomes.Methods Safer Spaces will use a mixed-methods approach combining participatory systems science with health economics methods to co-design and implement a ‘‘Safer Spaces’ Model of Primary Healthcare (SSMPH) targeting LGBTQ+ young people aged 12–25 years in rural Western Victoria. Phase 1 co-design of the SSMPH will be achieved through the establishment of a Queer Health Alliance, engagement in Group Model Building workshops via Deakin’s STICKE platform and the administration of a Discrete Choice Experiment to ascertain LGBTQ+ young people’s primary health service preferences. Phase 2 will implement strategies co-designed in phase 1 supporting primary healthcare for LGBTQ+ young people that are equitable, accessible and responsive to local needs. Implementation efficacy will be evaluated using participatory qualitative methods, systems-based monitoring (including causal loop diagrams and social network analysis) and stakeholder-led evaluation.Ethics and dissemination Ethical approval for this research project has been granted by Deakin University’s Human Research Ethics Committee. Safer Spaces will be developed in collaboration with lived experience researchers and the community. The knowledge translation plan will be integrated and revised throughout the project as partnerships and engagement with LGBTQ+ young people and their allies continue. All findings will be shared with rural health research bodies, policy makers, rural health providers and LGBTQ+ young people in ways that are meaningful to them.Discussion This protocol addresses critical gaps in rural health equity for LGBTQ+ young people by generating insights to guide community-informed service reform and building systemic capacity.