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Abstract Background While patient and family engagement in research has become a widespread practice, meaningful and authentic engagement remains a challenge. In the READYorNot™ Brain-Based Disabilities Study, we developed the MyREADY Transition™ Brain-Based Disabilities App to promote education, empowerment, and navigation for the transition from pediatric to adult care among youth with brain-based disabilities, aged 15–17 years old. Our research team created a Patient and Family Advisory Council (PFAC) to engage adolescents, young adults, and parent caregivers as partners throughout our multi-year and multi-stage project. Main body This commentary, initiated and co-authored by members of our PFAC, researchers, staff, and a trainee, describes how we corrected the course of our partnership in response to critical feedback from partners. We begin by highlighting an email testimonial from a young adult PFAC member, which constituted a “critical turning point,” that unveiled feelings of unclear expectations, lack of appreciation, and imbalanced relationships among PFAC members. As a team, we reflected on our partnership experiences and reviewed documentation of PFAC activities. This process allowed us to set three intentions to create a collective goal of authentic and meaningful engagement and to chart the course to get us there: (1) offering clarity and flexibility around participation; (2) valuing and acknowledging partners and their contributions; and (3) providing choice and leveraging individual interests and strengths. Our key recommendations include: (1) charting the course with a plan to guide our work; (2) learning the ropes by developing capacity for patient-oriented research; (3) all hands on deck by building a community of engagement; and (4) making course corrections and being prepared to weather the storms by remaining open to reflection, re-evaluation, and adjustment as necessary. Conclusions We share key recommendations and lessons learned from our experiences alongside examples from the literature to offer guidance for multi-stage research projects partnering with adolescents, young adults, and family partners. We hope that by sharing challenges and lessons learned, we can help advance patient and family engagement in research.