This report, developed by the Innovation and Value Initiative (IVI) and the EveryLife Foundation for Rare Diseases, outlines how comparative effectiveness research (CER), patient-centered outcomes research (PCOR), and value assessment must evolve to better reflect what matters to people living with rare diseases and their caregivers. Drawing on multi-stakeholder roundtables, a steering committee, and a targeted literature review, the project identifies common patient-centered outcomes across rare diseases—including physical functioning, fatigue, pain, mental health, social relationships, employment, sleep, and economic impacts—and highlights gaps in current research approaches. The report emphasizes seven cross-cutting themes such as the patient and caregiver journey over time, early and continuous engagement, data and methodological challenges, economic impacts, and the importance of scientific spillover. It concludes with consensus-driven recommendations for researchers, payers, and decision-makers to integrate patient and caregiver perspectives earlier, use mixed methods and broader outcomes, and adopt more flexible, equitable approaches to value assessment for rare disease treatments.