Rare diseases are usually complex syndromes, which sometimes cause extensive functional impairments affecting everyday life. The number of rare diseases and of people having one is increasing. Children with rare diseases often display special education needs and require support and adapted pedagogical methods to participate and achieve academic goals. The aim of this paper is to present a holistic educational working method for creating optimal settings for children with rare diseases, taking the dynamic interaction of biological and contextual factors into consideration and applicable to most rare diseases. It is based on over 20 years of practical implementation of a strategy for meeting the needs of children with rare diseases and their families. A research review about education for children with rare diseases, published between 2017 and 2021 is also presented. The results show that rare diseases often have educational consequences and that a holistic educational method, applicable to most rare diseases, is needed, but lacking. To contribute to a high-quality inclusive education teachers must understand how the origin of needs, including medical facts, their consequences and appropriate adjustments are closely linked.