The unexpected outbreak of the COVID-19 disease had significant and enormous repercussions on the healthcare systems, such as the need to reorganise healthcare organisations in order to concentrate resources needed to the care of COVID-19 patients and to respond in general to this health emergency. Due to these challenges, the care of several chronic conditions was in many cases discontinued and patients and healthcare professionals treating these conditions had to cope with this new scenario. This was the case of the world rare diseases (RDs) that had to face this global emergency despite the vulnerability of people with RDs and the well-known need for high expertise required to treat and manage them. The numerous lessons learned so far regarding health emergencies and RDs should represent the basis for the establishment of new healthcare policies and plans aimed at ensuring the preparedness of our health systems in providing appropriate care to people living with RDs in the case of eventual new emergencies. This paper aims at providing pragmatic considerations that might be useful in designing future actions to create or optimise existing organisational models for the care of RDs in case of future emergencies or any other situation that might threaten the provision of routine care. These policies and plans should benefit from the multi-stakeholder RDs networks (such as the European Reference Networks), that should join forces at European, national, and local levels to minimise the economic, organisational, and health-related impact and the negative effects of potential emergencies on the RDs community. In order to design and develop these policies and plans, a decalogue of points to consider were developed to ensure appropriate care for people living with RDs in the case of eventual future health emergencies.