Inclusive education of disabled students has been promoted in European disability policies. However, the transition process from more segregated system is slow. The purpose of this study was to provide an insight about different types of schooling of disabled children affected by a rare disease across Europe and to evaluate their and caregivers' well-being. We analysed data from a cross-sectional study (BURQOL-RD) of persons with rare diseases that cause intellectual and/or physical disability: Prader-Willi syndrome, fragile X syndrome, three types of mucopolysaccharidosis and Duchenne muscular dystrophy. The sample consisted of 359 children aged 6-17 and 269 caregivers from eight European countries. Results showed differences between countries in proportion of students placed in special schools, which are still valid option in countries such as Germany, France or UK. Within the inclusive education modalities, lack of special support for disabled students was observed especially in low-income countries. No association between the type of schooling and quality of life was observed, but the subjective caregivers' burden seems to be higher in special schools. The study shows existent differences in implementation of inclusive education in Europe. More research is needed in the field of rare disease disability and educational needs.