Ageism in healthcare has received increased attention in recent years, but literature focusing on how it affects individuals living with rare diseases remains scant. The rare disease population already faces obstacles when navigating health systems, and ageism has the potential to exacerbate existing health inequities. We conducted a systematic review of peer-reviewed and gray literature on health inequities in rare disease populations, seeking to identify publications that reported primary or secondary data on the equitable or inequitable treatment of these populations, or that discussed related regulatory, moral, or philosophical issues. Our aims were to understand how health inequities in these populations arise, how they are justified from societal points of view, how they manifest themselves in laws and regulations, and what effects they have on health care access and health outcomes. We retrieved information from 63 publications, which we inductively synthesized into five categories: ethical discussions, societal preferences, regulations, access to care, and health outcomes. Integrating insights from these categories, we developed an Ethical Spectrum and Resource Allocation Framework, which explains the emergence of equity issues and how they are manifested in health systems. By providing a better understanding of the root causes of health inequities, particularly among older adults, the framework can inform health policymaking, improving access to care and health outcomes for rare disease patients.