Objective: Research addressing the co-occurrence of autism (and/or neurodiversity) and gender-diversity (A/ND-GD) has been conducted largely without the perspectives and voices of the A/ND-GD community. Including A/ND-GD community advocates as research partners may be a critical next step for advancing research initiatives on the co-occurrence given the apparent complexity and alterity of the A/ND-GD experience. Method: Consistent with the community-based participatory research (CBPR) model we propose herein, our authorship team includes a partnership between clinician researchers and diverse A/ND-GD community collaborators. Multiple facets of the A/ND-GD lived experience are examined, including through narratives provided by our A/ND-GD community partners. Results: Based on our experience conducting A/ND-GD-related research and our lived experience as A/ND-GD self-advocates, we highlight challenges in this line of research, including risks of conducting studies without the involvement of the A/ND-GD community. And given that many A/ND-GD youth present with gender-related urgency during the teen years, we provide a developmental framework for how CBPR-informed methods may enrich our understanding of the care needs of these young people and provide context for the apparent heterogeneity in their gender needs and trajectories over time. Conclusions: Integrating CBPR methodologies in A/ND-GD research initiatives has the potential to optimize the relevance of the research questions asked and the interpretation and contextualization of study findings.