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Introduction Young adults with chronic autoimmune conditions face unique and often overlooked challenges in post‐secondary education due to the invisible and unpredictable nature of these conditions. This patient‐led qualitative study aims to further understand the experiences of young adults living with chronic autoimmune conditions while attending or considering attending post‐secondary education. Methods The study followed the three‐phase Patient and Community Engagement Research (PaCER) approach, a participatory framework that trains individuals with lived experience to lead all stages of research. In the first stage (SET), the protocol was co‐designed with three external patient‐partners. Study participants included young adults (18–35 years) with a chronic autoimmune condition for > 1 year who considered attending or attended a Canadian post‐secondary school within the last 5 years and were recruited through social media. Data were collected (COLLECT) via focus group and interviews and then analysed using thematic and narrative analysis. Findings were shared back with study participants (REFLECT) for refinement and to inform recommendations. Results Ten young adults participated, and eight key themes were identified. Themes included the wide‐ranging impacts of disease management, the value of peer and family support, protective and risk factors for success, limited awareness and education around chronic conditions, and sometimes‐unconscious burden of navigating invisible conditions. Participants also reflected on their resilience and the shifting accessibility landscape during Covid‐19, and offered detailed feedback on current gaps and needed support. Their recommendations underscored ongoing institutional shortcomings and the need for systemic change. Conclusion Our findings indicate that young adults living with chronic autoimmune conditions are not having their needs sufficiently met while navigating the post‐secondary education system. It is imperative that changes and feedback provided by students with lived experience are implemented to ensure an accessible post‐secondary education experience. Patient or Public Contribution Seven PaCER researchers, who identify as young adults with lived experience of chronic conditions, led the study design, data collection, analysis and manuscript preparation. This study was also co‐designed with three external patient‐partners who also identify as young adults with chronic conditions.